She was awarded the Jawaharlal Nehru Fellowship in 1976. Thapar is an Honorary Fellow at Lady Margaret Hall, Oxford, and at the School of Oriental and African Studies (SOAS), University of London. She holds honorary doctorates from the University of Chicago, the Institut National des Langues et Civilisations Orientales in Paris, the University of Oxford, the University of Edinburgh (2004), the University of Calcutta (2002) and recently (in 2009) from the University of Hyderabad. She was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 2009. She was also elected an Honorary Fellow of St Antony's College, Oxford, in 2017.