Bharathiraja started his film career as an assistant to Kannada filmmaker Puttanna Kanagal. Later, he assisted P. Pullaiya, Krishnan Nair, Avinasi Mani, and A. Jaganathan. His first film 16 Vayathinile for which he wrote the script broke the then existing convention to create a new genre of village cinema. The movie is now regarded as a game-changer and a mile-stone in the modern history of Tamil Cinema. About the movie, said Bharathiraja in his own words, "This movie was meant to be a Black & White art film produced with the help of National Film Development Corporation", but turned out to be a commercially successful color film and a starting point for several important careers.
His next film Kizhake Pogum Rail produced similar results and eventually brought in criticisms that Bharathiraja was capable of catering only to village audiences. This led him to make Sigappu Rojakkal, about a psychopathic woman hater that was totally Westernized in terms of both conception and production. But contrary to what several observers expected, this film met with box office success and everyone agreed that Bharathiraja was here to stay.
Bharathiraja confirmed his versatility and refusal to be tied down to one particular genre with an experimental film Nizhalgal and an action thriller Tik Tik Tik. But, undoubtedly rural themes proved to be his forte as his biggest hits in the 1980s Alaigal Oivadhillai, Mann Vasanai and Muthal Mariyathai were strong love stories in a village backdrop. Muthal Mariyathai starred veteran actor Sivaji Ganesan in the lead, playing a middle-aged village head. Radha is a poor young woman who moves into his village for a living. The love that bonds these two humans separated not just by age but also by caste and class, is told by Bharathiraja with poetic touches.
Vedham Pudhithu dealt with the caste issue in a stronger manner. The film's narrative was seamless and starred Sathyaraj as Balu Thevar. It contains some of Bharathiraja's trademark touches as well as several ground-breaking scenes. However, it does follow the anti-Brahmin trend common in Tamil films – in this respect it departed from his earlier success, Alaigal Oiyvadhillai, where the caste and religion factor was given a more balanced treatment. Bharathiraja has successfully managed to modernise his film making techniques for the 1990s. The commercial success of Kizhakku Cheemaiyile and the awards Karuththamma garnered stand as testimony for his ability to thrill the younger generation as well. Bharathiraja was on the same stage in 1996 to receive another National Award for Anthimanthaarai.
In late 1996, Bharathiraja was signed on to direct two films, with the Sarathkumar-starrer Vaakkapatta Bhoomi announced in October. The following month, he began work on a film titled Siragugal Murivadhillai with Napolean, Heera Rajgopal and Prakash Raj in the leading roles. Both films were later shelved.
He has plans of making short films with varying themes to attract the international audience and has currently completed his latest venture Kadal Pookal and picked up a national award for the best screenplay writer for the same film. The well-known Tamil film director Bhagyaraj was one of his assistant directors. He has also directed movies in Telugu, Kannada and Hindi.
He attended the Heroes Day conference at Jaffna and appreciated its heroism and valour. Tamil Nadu Congress president Krishnasamy claimed he met the LTTE's leader, Prabhakaran, accused of planning the assassination of former Indian Prime Minister Rajiv Gandhi and banned in India.
He organised a protest by Tamil Nadu artistes against the Indian state of Karnataka for not releasing Cauvery water at Neyveli. During a SUN TV interview, co-film stars like Sarath Kumar and Radhika who attended the conference accused him of using that opportunity to eulogise current Tamil Nadu chief minister Jayalalitha and launching attacks on Rajinikanth's ethnicity.
In the month of June 2013, it was claimed that Bharathiraja was responsible for the death of Manivannan. Bharathiraja made harsh comments against Manivannan in a leading Tamil magazine.