Mukherjee resigned his powerful role as federal finance minister last month to run for the largely ceremonial position that has a 5-year term, NDTV reported.
India's president is elected by thousands of politicians, rather than the population.
Election officials said Mukherjee took more than 69 percent of the votes Sunday.
A formal swearing-in ceremony was scheduled for Wednesday.
Mukherjee is leader of the Congress Party, which heads the governing coalition parliamentary government. He has also served as the country's minister of foreign affairs and defense.
While his presidential role is mostly ceremonial, Voice of America said he could play a significant role in next year's general elections.
Various polls and analysts suggest there won't be a majority victory in the parliamentary vote, in which case the president determines the political pecking order.
Mukherjee is India's 13th president and replaces the country's first female to hold the post, Pratibha Patil, the BBC said.