Mukherjee, was elected to a five-year term by members of the national and state parliaments in voting that began Thursday. The position is largely ceremonial, but he could help determine who forms the next government after elections in 2014 if there is no clear winner.
Mukherjee replaces Pratibha Patil, who was India's first woman president. He defeated Purno Sangma, a former speaker of the lower house of parliament who had the backing of the opposition Bharatiya Janata Party.
The 2014 elections are not expected at this point to produce a clear result, in which case the president could play a decisive role.
Mukherjee's victory will come as a big boost to the Congress Party, which has been under pressure over a series of corruption scandals and a slowdown in the Indian economy, the BBC reports.
Mukherjee has headed several top government ministries during his career, including the foreign, home, defence and trade ministries.