Amidst the picturesque hills of Sultanpur, Azad Kashmir, Pakistan lives a six-year-old mute girl named Shahida. One afternoon, she is playing on a hill when she accidentally falls off it. When she doesn't return home by the end of the day, the villagers organise a search party. After hours of searching, they find the little girl on a branch protruding from the hill. She had been stuck on it for the entire day but couldn't call for help because of her disability. The following morning, her parents and neighbours discuss what must be done to help her. An older man suggests they take her to the shrine of Sufi saint Nizamuddin Auliya in Delhi, India. The religious family believes that visiting the holy shrine will bring peace and happiness and most importantly, restore Shahida's speech. Shahida's father, being an ex-armyman, is sure that he won't be provided with a visa to India. Hence, her mother Razia takes it upon herself to travel far from the village for the first time. The trip goes as planned for the most part. The two reach the shrine, pay for offerings and get on a train back to their home country.

On the return journey, the train stops for repairs at night. When everyone is asleep, Shahida notices a sheep stuck in a pit right outside the train. She doesn't think much before going outside to help the animal. However, the train restarts before she can return to her mother. The little girl runs towards it but is eventually left behind, and in a desperate attempt to go the same way that her mother did, she boards a freight train. But to her dismay, it goes reverse-path and stops in Kurukshetra, India. Razia notices her daughter is missing and stops the train. Policemen are appointed to look for the girl around the track where she was lost. However, they cannot find her since Shahida has already reached a different place. Razia meets her husband who is worried to death about his daughter. They cannot get an immediate visa back to India, much to their dismay. The parents have no other way but to pray that their daughter is safe.

Meanwhile, Shahida is now lost in a different country with no way to communicate. At a religious celebration, she sees a stranger eating at a street-side restaurant. The stranger is the kind Pawan Kumar Chaturvedi who invites her to have a meal with him. After a few minutes of trying to get her to talk, he realises she is mute and starts calling her Munni. A starving Munni finishes the food and follows Pawan around. Assuming that she was separated from her parents during the festival, he asks her to stay in front of a temple. Pawan is a devout Hindu Brahmin and an ardent devotee of Lord Hanuman. He believes that Lord Hanuman will take Munni home if she stays in front of his temple. When Munni still doesn't stop following him, he brings her to the police station. But since she cannot tell them any details about her parents, the police can only wait for someone to file a missing complaint. Until her parents are found, Munni needs a place to stay, hence, Pawan takes her in. On his way to his home in Delhi, he tells Munni to call him Mama if she ever talks in the future. He also starts naming different Indian cities, asking her to nod if she knows what city her parents are in. All the passengers on the bus help him but none of them name cities outside of India. As they talk, Pawan tells everyone how he came to Delhi for work.

A flashback shows the time he was in high school. He was an average student who could never pass the final examination. All his friends cheated and went …

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The film's story writer V. Vijayendra Prasad stated that the idea of the film was inspired by the 1987 Telugu film Pasivadi Pranam, which itself is a remake of the Malayalam film Poovinu Puthiya Poonthennal (1986). Prasad also took inspiration from a story he heard about a Pakistani couple coming to India for their daughter's heart surgery. It has also been noted that the core plot is equivalent to that of the 2006 Kannada movie Kallarali Hoovagi.

Kabir Khan noted that the script of Bajrangi Bhaijaan was influenced by some of his own experiences. He noted the influence of the Hindu epic Ramayana, which he used to watch Ramlila plays of as a child, and particularly the Hindu deity Bajrangi (Hanuman), who left a strong impression on him as a child. He felt that Bajrangi was a character who was loved by people all religious communities in India, including Hindus and Muslims in India, due to how Bajrangi brought joy and fun to many Indian children. Khan began writing Bajrangi Bhaijaan partly in response to the rise of religious sectarianism in India since the 1980s and particularly in response to the Bajrang Dal, a Hindu fundamentalist organisation that appropriated Bajrangi for violent sectarian motives and played a central role in the deadly 2002 Gujarat riots, leading to the name Bajrangi having communal connotations. He began writing Bajrangi Bhaijaan in 2013 as a way of reclaiming Bajrangi for all communities, and as a way of bringing Hindus and Muslims together.

The film's casting director was Mukesh Chhabra.
The principal photography began on 3 November 2014 in New Delhi, with Salman Khan and Kareena Kapoor Khan participating. The second filming schedule took place at the ND Studios, Karjat. The third schedule of the film was held in Mandawa, Rajasthan. On 7 January 2015, Khan was seen on the top of the castle of Mandawa playing cricket with a young boy. On 10 January 2015, Khan shot with school students in Rajasthan's Jhunjhunu district. Shooting of the film was completed on 20 May. Some scenes of the film were shot at Khan's Panvel farm house. Shooting also took place in the Kashmir Valley in places like Sonamarg and Zoji La. The film's climax was shot at Sonmarg near the Thajiwas glacier (at 10,000 ft above sea level) with around 7,000 people. Nawazuddin Siddiqui's character Chand Nawab was inspired by a real character Chand Nawab, who was with Karachi-based Indus News in 2008.

A. R. Rahman was initially in talks to compose the music of the film, however he did not sign the film. The music was then composed by Kabir Khan's usual collaborators, with Pritam composing the songs and Julius Packiam composing the score. The lyrics were written by Mayur Puri, Amitabh Bhattacharya, Neelesh Misra, Shabbir Ahmed, and Kausar Munir while Julius Packiam composed the score. The soundtrack of the movie become Super Hit. The Song "Bhar Do Jholi" one of the biggest hits of 2015 sang by Adnan Sami. The soundtrack album consists of eleven tracks, was released on 17 June 2015. "Tu Chahiye" and "Selfie Le Le Re" become chartbusters.

The film includes the qawwali "Bhar Do Jholi Meri Ya Muhammad" originally written by Purnam Allahabadi and composed and sung by the Sabri Brothers. The qawwali was revamped with the voice of Adnan Sami Khan and partly includes "Dam Ali Ali". EMI Pakistan and Amjad Sabri heir to the Sabri Brothers, have called for legal action against the producers of the film and the qawwali in separate instances.