An alien (Aamir Khan), with a body similar to the human body, lands on Earth for a research mission on the human world. He gets stranded in Rajasthan as his spaceship's remote control device gets stolen by a villager. The alien chases the man in an attempt to retrieve his device back but only manages to take the radio recorder of the thief. He later learns that roaming naked on Earth isn't deemed natural. Thus, he begins stealing clothes and money from couples having sex in cars with open windows.
The alien befriends Bhairon Singh (Sanjay Dutt) who assumes the alien is simply a person suffering a memory loss. Singh helps the alien get accustomed to the village. The alien has the ability to transfer a person's memory to his own brain by holding that person's hands and, hence, he attempts to learn the local language through this technique. However, he finds out that just grabbing the hands of a stranger, whether male or female, is not accepted, and since he does not speak the language yet, he is unable to explain what he wants. Singh, who interprets this alien's behavior as sexual interest, takes him to a brothel. Over there, the alien holds a prostitute's hand for several hours, and thus learns the language.
The alien travels to Delhi as he is informed that it is most likely the place where his stolen device would be sold. Due to his strange behaviour, the people in the city assume him to be tipsy and refer to him as PK. Delhi turns out to be a very large city, and people tell him that only God can help him find the device. However, PK is confused by the various religions and their own different understandings of God. PK later discovers that a godman, Tapasvi Maharaj (Saurabh Shukla), has his device. However, the godman falsely claims to have attained it from the Himalayas, and refuses to return it to PK.
Meanwhile, TV reporter Jaggu (Anushka Sharma) meets a man named Sarfaraz (Sushant Singh Rajput) while both are in Bruges. Although Jaggu's father is strongly against a relationship between them due to Sarfaraz being from Pakistan, Jaggu decides to marry Sarfaraz anyway in Bruges. While she waits for Sarfaraz in the town hall, a boy delivers a letter to her that states that the marriage is off due to their differences, with a request to refrain making contact. Jaggu, very disappointed, leaves, discarding the letter by leaving it there on a chair.
Later, back in India, Jaggu sees PK distributing leaflets about a missing God. As a reporter, she is interested in this strange man, and makes contact. PK tells her the whole story. Jaggu convinces her channel head (Boman Irani) to make a TV show with PK, exposing Tapasvi. People in masses get connected to the show and open their eyes against the fake godmen. Tapasvi comes to the studio for a confrontation with PK. In the same TV show, Tapasvi brings up Jaggu´s personal matter of her bad experience with Sarfaraz to prove a point. Due to PK's request, Jaggu reluctantly tries to contact Sarfaraz which leads her to call the Pakistan Embassy in Belgium. The embassy tells Jaggu that Sarfaraz calls them daily to inquire whether Jaggu has called. It turns out that the message in Bruges was a case of mistaken identity by the letter delivery boy. After Jaggu left the town hall, Sarfaraz had arrived and assumed the message was from Jaggu, for him. The misunderstanding between them gets cleared. After hearing this, Tapasvi reluctantly gives PK his device back.
In this whole process, PK falls in love with Jaggu but chooses not to tell her as she loves Sarfaraz. Recording tapes with her voice in them, he fills his suitcases with batteries to be constantly able to hear them on his home planet. While departing, he lies to Jaggu regarding the content of the tapes. Jaggu, having found out the true content of the tapes, painfully keeps quiet.
Jaggu later publishes a book about PK and, at a book reading, claims that she misses him deeply due to the memories he has left her with and the impact he had made on her life.
The movie ends with PK coming back on Earth a year later for more research with another alien (Ranbir Kapoor).