Sujatha served as the Union Secretary in the Ministry of Health and Family Welfare for the Government of India until 2010. She was involved in several key projects: the first ever national program for non-communicable diseases, the process for a national policy for use of antibiotics and introducing vaccines in public health.

From 2006-09 she was the Director General of the National AIDS Control Organisation (NACO) and represented India on the boards of WHO, Global Fund and UNAIDS.
Sujatha is the first Gro Harlem Brundtland Senior Leadership Fellow at Harvard Schools of Public Health.