Pinjar tells the story of Puro, a young woman of Hindu background, living a lovely life — circling the time of the partition of 1947 — with her family. Puro is betrothed to a wealthy, sweet young man, Ramchand, from a promising family. Puro's bliss is shattered one day as a leisurely trip with Rajjo, her younger sister, turns traumatic as she is kidnapped by a mysterious Muslim man, Rashid. Rashid's family has an ancestral dispute with Puro's family. Puro's family had made Rashid's homeless by taking over their property. Puro's grand-uncle had even kidnapped Rashid's grand-aunt and then released her after defiling her. Rashid's family made him swear that he would kidnap Puro to settle the score.
It is clear that Rashid is drawn to Puro and would do anything for her. One night, Puro manages to escape and return to her parents. Her parents woefully turn away their daughter, explaining that if Puro were to stay, Rashid's extended Muslim clan would slaughter everyone. Left with no support, Puro returns to Rashid who is well-aware of Puro's escape; he knew she wouldn't be let in by her parents and had been waiting for her nearby. After a few months, Puro's family marries their son Trilok to Ramchand's younger sister, Lajjo while Rajjo is married off to Ramchand's cousin. Meanwhile Rashid marries Puro (Hamida), they adopt a child,found on the road, and treats him with much affection and love. But when the village people come to know that the child belonged to a Hindu background, they take him away from the couple.
The British colonialists leave India and the subcontinent reels under the effects of partition. Ramchand's uncle, cousin and Rajjo leave for India and are safe. Ramchand, his parents and Lajjo are caught in the riots. Ramchand hurriedly leaves to India with his younger sister and mother; his father is already missing. Shortly after, Lajjo is kidnapped by thugs. Puro meets Ramchand, who woefully tells her of Lajjo's situation. Puro finds Lajjo and helps her escape with Rashid's assistance. They send Lajjo to Lahore where Trilok and Ramchand come to receive her.
Trilok has a tearful reunion with Puro and explains to her that she can start life anew as Ramchand is ready to accept her even now. Puro surprises Trilok by refusing and saying she is where she belongs. Ramchand responds with tremendous empathy to Puro, as he sees that she has accepted Rashid. Rashid slowly tries to fade, making it easy for Puro to leave with her folks, but is heartbroken, as he is deeply in love with her. However, Puro seeks Rashid out and the two tearfully bid Ramchand, Trilok, and Lajjo farewell forever.