In 1972, while working on her doctoral thesis, Mukherjee was hired by the Centre for Historical Studies, JNU, as a faculty member, from where she retired as a professor of history. She was a chairperson of the Centre as well. In 2005, she was appointed as the director of the Nehru Memorial Museum and Library, New Delhi.
Research
She investigated agrarian history in the Punjab. She argued that despite extensive irrigation works, colonialisation caused agricultural involution, with the number of workers per unit area rising and production dropping. She also analysed peasant movements in the erstwhile princely states of the Punjab across the pre- and post-1947 periods. Her critical analysis of a Marxian orientation of peasant consciousness has been highlighted. A common thread running through Mukherjee's work has been a criticism of the Subaltern mode of historical inquiry, which informs her analysis of peasant movements as well as her other major contribution: modern Indian history. This is encapsulated by the two books co-written with Bipan Chandra et al: India's Struggle for Independence and India after independence: 1947-2000. In the former book, the authors sought to "demolish the influence of the Cambridge and Subaltern 'schools' reflected in the writing on colonialism and nationalism in India".
Ideology
After Mukherjee was appointed as the director of the Nehru Memorial Museum and Library two letters, written between February 2008 and June 2009 and signed by various academics, including Ramchandra Guha and Sumit Sarkar were sent to the NMML's executive council complaining of alleged deterioration in scholarly standards of the centre. Supporting Mukherjee, another set of academics, including Irfan Habib and Madhu Kishwar, wrote to the Prime Minister of India protesting her treatment. Mukherjee herself pointed out that under her tenure, the NMML had completed a ten-volume publication of the selected works of Jayaprakash Narayan, besides initiating a digitisation project. The executive council disregarded the petition and extended Mukherjee's tenure for another two years. Following the end of her appointment, a search for her replacement ended up in a court case with accusations of irregularities. The Delhi High Court struck down the appointment of Mukherjee's successor on the grounds that the process was faulty and against norms.
