S Regunathan joined the Indian Army as a Commissioned Officer. He put in five years of service in the army before joining the Indian Administrative Service where he was allotted to the 1968 batch. 

He has held many appointments from administrator, collector to Secretary of revenue, finance home, transport, tourism, education and information technology.

As Secretary education, Government of Delhi he spearheaded the Sarva Siksha Abhiyan movement in Delhi with 40,000 volunteers. 4 lakh adults and children were educated in the period of 1994-98. During his tenure, he also brought in information technology to the education department and created Pratibha Vidyalayas for bright government school children. He established the Indraprastha University during his tenure and was also instrumental in the setting up of Amebedkar Uiversity, Delhi.

As Commissioner, Transport, Delhi Government, he was a major force in bringing metro to the Delhi. As Chairman, Delhi Tourism, he established Dilli Haat in collaboration with NGOs.

Regunathan was also Vice Chancellor of Arunachal Pradesh University for a year. He held the post of Principal Secretary to Chief Minister in Delhi from 1998-2004 and then he moved to the Govt of India as Secretary in the Ministry of Agriculture but returned to Delhi govt. as Chief Secretary, a post he held from 2004-06.  He was also Advisor to the National Knowledge Commission.

Presently he is the Chairman of the Balwant Rai Mehta Vidyalaya, a school functioning under the aegis of Servants of People Society, catering to the needy and differently abled sections of society. He was, earlier, for a short duration, Vice President of the Foundation for the Restoration of National Values. He is a keen golfer and loves to listen to music.