In August 1947, after India sought independence from the British, the Last Viceroy of India, Mountbatten gave Cyril Radcliffe, the responsibility of dividing India into two parts – India and Pakistan. Radcliffe drew two lines – one in Punjab and another one in Bengal. This line was known as the Radcliffe Line.
Begum Jaan (Vidya Balan) is a prostitute who runs a brothel between the cities of Sakkergarh and Dorangla. The prostitutes in Begum Jaan’s brothel are a number of girls she raised herself, who were either abandoned or disowned by their families and now work for her. The members of the brothel include an elderly woman known as Amma (Ila Arun), Sujeet (Pitobash Tripathy), a local worker who brings her customers and Salim (Sumit Nijhawan), a gunman who guards them and also two dogs. They are pestered by government officers Hari Prasad (Ashish Vidyarthi), Iliyas Khan (Rajit Kapoor) and Inspector Shyam Singh (Rajesh Sharma) who visit her and ask all of the residents to evict the brothel, as it lies on the land that the Radcliffe Line is to pass through. Love is shown to blossom between Sujeet and Rubina (Gauhar Khan). Begum Jaan’s brothel is looked after by Raja Saab (Naseeruddin Shah), under whose protection, they are safe and sound. He pays their taxes and duties. Begum Jaan sends message to him for his help in this matter. He arrives at the brothel with gifts and presents for them and after hearing about their plight, he assures them of help by stating that he would be going to Delhi soon and discuss the matter there. However, he demands to spend the night with young Shabnam (Mishti Chakraborty), who had recently joined the brothel as a mental wreck after abuse. Begum Jaan reluctantly forces Shabnam to sleep with Raja Saab while she sings in the sidelines as he enjoys his night.
After several failed attempts to convince Begum Jaan and her team to leave despite giving them a month’s notice, as a last resort, Hari and Iliyas, enlist the help of Kabir (Chunky Pandey), an infamous killer in Sonapur, to threaten Begum with her members to vacate the brothel. Raja Saab returns to the brothel one day to inform Begum Jaan that his efforts to save her brothel have failed and now she must vacate the brothel. Begum, who was having hopes from Raja Saab is shocked in dismay. Still, she stubbornly tells Raja Saab come what may, she’ll rather die in her house like a queen than die on the streets like a beggar. Kabir proceeds to kill Begum’s beloved dogs, even feeding their meat to Begum and her girls. He then kills Sujeet while he is returning from the market with a few other girls of the brothel. He persuades the girls to escape while sacrificing his life. This killing enrages Begum Jaan and her members further. As a result of Kabir’s intimidation tactics, Begum asks Salim to train every one of her girls to use weapons and fight back. Intensive training practice sessions are held.
Meanwhile, Masterji (Vivek Mushran), Laadli’s teacher, is in love with Begum Jaan and proposes to her, unaware that another prostitute named Gulabo (Pallavi Sharda), harbors feelings for him as well. Begum Jaan rejects his proposal and asks him to leave, leading an irate Master to concoct a plan to kill her. He convinces Gulabo to run away from the brothel, betraying Begum Jaan. Gulabo does so but Masterji spurns her and gets her raped by his accomplices inside a horse carriage. She vows vengeance.
That same night, Kabir and his men attack the brothel. Begum and the girls fight back but to no avail. Gulabo returns back and later slits Masterji’s throat, while he is witnessing the attack on the brothel by Kabir and his goons. However, she has been badly assaulted by Masterji’s accomplices and dies. The goons throw lighted torches inside the brothel, causing the building to be engulfed in flames. Begum Jaan and her girls put up a determined fight. Many are killed. She and her four surviving members smile while looking at their home being set ablaze; they walk inside the building and shut the doors. They burn to death as Amma narrates the story of Rani Padmavati of Chittorgarh, who refused to fall into the hands of the enemy and instead martyred herself and died a valiant death, just like the plight of Begum Jaan.
As the movie ends, Illiyas, Hari Prasad and Shyam Singh are seen to be remorseful of their actions; Illiyas shoots himself and we are shown the remains of the brothel and the end to Begum Jaan’s legacy.