The film begins with a montage of landscapes. Then we see a painting, which looks just as realistic as the cinematography we have just seen. The artwork is observed by Gerda Wegener (Alicia Vikander). It is revealed that she is attending an art show when a patron comments that Gerda's work is not as exquisite as her husband's, the artist of the painting Gerda was admiring. The gallery owner declares Gerda's husband, Einar Wegener (Eddie Redmayne), to be part of the one percent of gifted Danish talents.A title card reads that it is the year 1926 in Copenhagen, Denmark. Einar and Gerda walk home from the art show together. She makes fun of the man declaring Einar part of the one percent. A man shouts down at them to be quiet because it's late at night. They laugh and hurry home.The next morning, Gerda is painting a man's portrait. Simultaneously, Einar visits their friend, Oona Paulson (Amber Heard) at her ballet class. He says he wants to give Gerda space to work and his presence would be distracting. At their home, Gerda tells a middle-aged man who she is painting that men tend to be afraid of the gaze of a woman.Einar is working on a painting of his own, of five trees in the woods, an actual sight in their town. His paintings take much longer to complete than hers, as he is very meticulous at detail. Einar and Gerda are affectionate with each other and they begin to have sex. While she is undressing, he asks her to leave her undergarments on as he finds them beautiful. He caresses her clothes and then they make love.Gerda is finishing a large portrait of a woman but Oola is supposed to serve as her model and she has not arrived. She asks Einar to wear the stockings and shoes so that she can finish painting that part of the picture. He nervously agrees and she has to educate him on how to put the stockings on. She then has him hold the dress up so that it will flow over the stockings properly. Just then, Oola shows up with flowers. She is delighted at the sight of Einar serving as the model and hands him a lily, telling him that that must be his name.Gerda meets with an art collector to evaluate her portraits and paintings, including the one with the stockings. He tells her that sketches of people are commonplace and there is nothing unique about them but she is a good artist who just needs a better subject.When Gerda returns home, she explains the feedback she received to Einar. They begin to kiss and she begins to take off his shirt. Underneath, he is wearing her undergarments. This takes her aback but she doesn't acknowledge it directly and instead, she simply continues touching him underneath the brassiere he is wearing.In the morning, Gerda sketches Einar while he sleeps but in an androgynous way so its not clear if the picture is supposed to be of a male or female. When he wakes up, she tells him how beautiful he is.The next day, Gerda and Einar join Oola for a gathering. Oola tells them that she has had relations with two nearby men at the same time. They are stunned by this and she giggles that its so easy to shock married people. Gerda tells Oola how Einar and her first met when he admired her ankles. He was too shy to ask her out so she did it for him. He was so beautiful that when they kissed, she felt as if she was kissing herself (another woman). This makes Oola blush and Gerda comments that its so easy to shock unmarried people.There is an event that Gerda and Einar are invited to but he doesn't want to go because the people gush over him as an artist. Gerda realizes that he can go in disguise, as Lili. Gerda puts makeup on Einar's face and finds a wig for him. He has transformed and he delights at being able to inhabit the identity of a woman.They attend the party and everyone is told Einar couldn't attend but his cousin, "Lili", has taken his place. Lili is left on his/her own and she catches the eye of Henrik (Ben Whishaw) who is immediately intrigued by "her". They isolate themselves and Henrik flirts with Lili, who is awkward in response. Henrik tells her a man should always ask a woman before he kisses her and then leans in. She pulls away and says he didn't ask. But he tells her he didn't want her to refuse. Gerda walks in and witnesses the two clumsily kissing. Lili begins to have a nosebleed and becomes frightened. Gerda leads her away.At home, Gerda is confused about what she witnessed. She doesn't understand why the game they were playing went so far. Einar tries to explain that he didn't want to kiss Henrik but when he was in the mind of Lili, she did so it was Lili who wanted to, not him. Gerda asks if he has kissed boys before. He says only once, when he was very young with a friend of his. His father saw it happen and got very upset with him.Gerda now has found her subject: she paints Einar as Lili. When she presents these paintings to the art collector, he loves them and wants to have a show with them. The collector wants to meet the model but Gerda tells him it was Einar's cousin who has since left town. At home, Einar is wearing Gerda's undergarments as he looks in the mirror and studies his body. He strips himself bare and then finally removes his trousers. He looks at his penis with disgust and tucks it between his legs.When Gerda gets home to tell Einar of the praise the collector has given her Lili portraits, she is surprised to see Einar dressed as Lili. She wonders if something is the matter with him and suggests they go see a doctor. They do and the doctor makes notes of the nosebleeds, as well as the stomach cramps he imagines having once a month. Einar tries to explain he has always felt like a girl despite being in a male body.The next time Gerda meets the art collector, she is told he sold all the paintings and there is representation interested in her in Paris. He encourages her to go and become an esteemed artist in France. Gerda encourages Einar to join her, as she will need Lili as a model for her paintings. The two of them set out to live in Paris.In France, Einar continues to serve as the model for Gerda's portraits. They seem to be distancing themselves from each other. While Gerda is out that evening, Einar goes to the seedy part of Paris' red-light district and enters a peep-show club. He watches a woman strip naked. But instead of being aroused by her, he starts to mimic her movements. She notices this and they do a back and forth game where they mirror each other.Gerda goes to meet Hans Axgil (Matthias Schoenaerts), a childhood friend of Einar's. Hans tells someone on the phone he must go because he has a "Danish girl" waiting for him (interesting because the movie's title alludes to both Lili and Gerda). He tells Gerda he loves her artwork but he cannot represent her because he doesn't specialize in those kind of paintings. He asks to meet the model and she tells him it is Einar's cousin but she is not around. However, she tells Axgil that Einar is waiting for them at home though.When they get to the house, Einar is dressed as Lili. Gerda has to completely backpedal and explain that this is Einar's cousin and Einar is out. "Lili" brazenly flirts with Hans who is very suspicious. Lili becomes frazzled and runs off. When Gerda comes to join him, he tries to assure himself that Hans has not detected the reality of who he is.Gerda attends an art show for her Lili paintings. Hans is there and he tries to kiss her, knowing that her husband is a transsexual, but she stops him and tells him, "Einar is still my husband". Hence sets up a unique love triangle Hans loves Gerda who loves Einar who loves Hans. All of this overwhelms Gerda who leaves the event despite it pouring down rain, refusing an umbrella in lieu of walking down the street. Hans finds her and brings her to shelter.At home, the three are gathered in the kitchen. Hans reveals to Gerda that he was the childhood friend that had once kissed Einar. Einar was dressed in his grandma's apron while they were playing pretend. Hans thought Einar looked so pretty, he just had to kiss him. He was then sent home while Einar's dad violently responded to his son.Gerda wonders if she has turned Einar into a transsexual when she dressed him up for the event but he tells her he's felt like that his whole life and she merely gave him the first opportunity to experience it. Because he is still confused about his feelings, Gerda and Einar visit various doctors in Paris in hopes that they will be able to make sense of the situation. The first doctor suggests a lobotomy, telling Einar he will make two holes on each side of his head. The second one tells Einar that his diagnosis is bad that he believes Einar is a homosexual. The third excuses himself during the meeting. When Einar looks at his notes, he sees the man suspects that Einar is a schizophrenic. As the doctor rushes back to the office with a security team and a straitjacket, Einar escapes out a window.Oola is in Paris and she tells Einar and Gerda about a doctor who has treated a patient with the same situation as Einar. They meet with the doctor who is progressive and tells that he once met a man who believed he should be a woman, so he set to perform two operations the first, to remove his man bits and after he's recovered his strength, a second, to construct a vagina. But the man got scared and disappeared on the day of the surgery. Excitedly, Einar says that he wouldn't do that. And he agrees to have what will be the first sex change operation.Einar is standing in front of a train, to be taken to the hospital where the surgery will be performed. Gerda tells him she will be there for the surgery but he wants to be alone. Hans tells Einar, "I've loved only a handful of people and you are definitely two of them."Einar is admitted to the hospital. He is giddy with excitement and looks at himself lovingly in the mirror. He then decides not to put his wig on and to instead stylize his own hair in a feminine manner.On the patio of the hospital, a pregnant woman asks "Lili" if she is there because she is going to have a baby. Lili says maybe someday, not knowing what the limitations will be to the surgery (i.e., if she'll be able to get pregnant).The doctor goes over the procedure with Einar/Lili and she glows with anticipation. She tells the doctor she hopes her husband will be handsome like he is and mentions her hope of giving birth. The doctor warns that the surgery will be very brutal but Einar/Lili says she will sleep through it.The first surgery ends up being just as the doctor predicted brutal. Gerda arrive as a surprise, to support Lili. Although she is drained by the operation, Lili is also enthralled that it was performed. She is given estrogen pills to take every few hours but explicitly told to spread them out throughout the day.Although the surgery is only half done (Einar/Lili no longer has a penis but doesn't have a vagina yet), Lili enjoys living her life completely as a woman. Instead of painting, she gets a job as a sales clerk in a local department store. She shares some tips on how to apply perfume to customers, telling them that when she was in Paris, women never applied perfume directly on their skin. They would spray it in the air and then walk into it. This tip is well received.When Lili walks through a park, two local French men heckle her, calling her a lesbian and asking if she has a "hoo hah". When cornered, she punches one of them but the other one retaliates by badly beating up Lili.Gerda runs into Lili in the marketplace, where she is fraternizing with Henrik (the Ben Whishaw character she met when she was first dressed as Lili). Lili visits Gerda's home and tells her she is not romantically linked to Henrik because he is a homosexual. Gerda tries to encourage Lili to paint alongside her like they used to. But Lili is adamant that she has left Einar behind and no longer wants to do the things she did when she was living as a male. She then takes an estrogen pill, which upsets Gerda because Lili has just taken some ten minutes earlier (the doctor emphasized they have to be taken far apart). Lili defensively states that she knows what she's doing. Its obvious she wants to rush the process.Lili arranges to have the second part of her surgery despite Gerda telling her its too early. But the doctor agrees so she returns to the hospital and undergoes the procedure. Both Gerda and Hans are there for support but the doctor tells them the surgery did not gone well and the prognosis does not look good.Gerda and Hans visit Lili in the recovery room and she looks close to death. Nonetheless, she is happy and tells them, in a weak voice, that she finally feels like who she was meant to be. She adds that God made her a girl but there was some mistake in her physicality.Gerda takes Lili outside in a wheelchair so he can get out of the hospital room. Even though she is sick, Lili is happy. But despite her bliss, Lili passes away, leaving Gerda distraught.In the final scene, Hans and Gerda go walking through Denmark and stop at a set of five trees, the ones Einar had been painting early in the film. The scarf that Gerda is wearing blows away in the wind. Hans goes to retrieve it but she tells him to leave it alone. The piece of women's clothing floats in the sky, above the beautiful landscapes that Einar once painted, symbolizing that Lili was finally free.