Rajeev started his bureaucratic career as the Sub-Collector of Kollam. After working in various departments in the Government of Kerala, he served as the District Collector of Malappuram and Thrissur districts during 1994–96. At Malappuram, he piloted a community-based Self-help group program which was aimed at educating and empowering women to improve nutrition, child care, family health and micro-credit societies. This successful pilot—then known as the Malappuram CDS Model—contributed to the launch of state-level Kudumbashree program and the National Rural Livelihood Mission at the national level. Multiple stints in various departments in Kerala followed; he then served as a Consultant with National AIDS Control Organisation, National Programme Officer and National Technical Consultant at UNAIDS' India Country Office. During 2007–2010, Rajeev served as the Chairman of Kerala State Electricity Board. As the head of Rashtriya Swasthya Bima Yojana (2013–15), he revamped various processes to simplify health insurance access for India's poor. While at Ministry of Rural Development, he headed India's rural housing program—Indira Awaas Yojana—and the National Social Assistance Programme (NSAP) aimed at providing financial assistance to the elderly, widows and persons with disabilities in the form of social pensions. Since 2016, Rajeev, as an Additional Chief Secretary, heads Kerala's Department of Health and Family Welfare—his third stint as the head of this department in Kerala, the earlier stints being 1996–2001 and 2011–2013. He played a key role in controlling the situation during 2018 Nipah virus outbreak in Kerala. During the same year, Kerala was hit by unprecedented rains and floods. The health department under Rajeev played a crucial role in tackling the health situation that followed the 2018 Kerala floods.