Following the completion his PhD, Farooqi joined the National Gallery of Modern Art. After two decades of service, he was appointed director of the NGMA.[3] During this time, he began publishing a catalog that documented 3,000 of the then-14,000 works, including the artist's name, acquisition number, title, and medium.[4]
Dr. Farooqi has managed exhibition of artist and also archived the many artist work. He curated the exhibition Indian Women Sculptors in 1987.[5] Along with GM Sheikh and Geeta Kapur, Anis Farooqui organised the Birth of Modernity exhibition for the Festival of France in India at the NGMA in 1989.[4]
Dr. Farooqi’s artworks are included in several notable collections. These include the National Gallery of Modern Art in New Delhi,[6] State Lalit Kala Akademi in Utter Pardesh,[7] and Sahitya Kala Parishad in Delhi. His works are also part of the collections at the Punjab Government Museum[8] and the Punjab University Museum in Chandigarh.[9] Other institutions that hold his work include the British India Corporation in Kanpur, Ghalib Academy,[10][11] Doordarshan, and the Institute of Medicine and Medical Research in New Delhi.
His academic work has been part of course work in the Faculty of Arts at several institutions and board including CBSE and Punjab University, Jamia Millia Islamia etc. His book 'Hindustani Masavri' was the part of fine arts curriculum in senior secondary examination of CBSE till 2012.[12][13] His another book 'Art of India and Persia' was the output of his doctoral thesis.[14][15][16] He has written sketch of the personalities of many artists including Sayed Haider Raza, MF Hussain, Satish Gujral, Nalini Mehta and others.[17] In 1985, he along with Culture Secretary of Karnataka Govt Chiranjeev Singh, and through their combined efforts, they initiated the establishment of the NGMA Bangalore.[18]