The name was selected through a contest on 'Mygov' website launched by Modi last month to enable common people to share their thoughts and ideas.
It was chosen after scrutinizing 6,000 entries from all over the country.
Under the scheme announced by Modi in his Independence Day speech, poor people will get bank accounts with debit cards along with an insurance cover of Rs one lakh each.
Sharing the genesis of the name, the Prime Minister thanked all those who had participated in the contest.
"Glad to share that the name of Financial Inclusion Scheme, 'Jan Dhan Yojana' was selected through a contest on MyGov," Modi tweeted.
"Congrats to all participants who have given their inputs and hope all of you keep sharing your inputs on 'MyGov' in future too," he added.
More than 6,000 entries were received during the contest. A jury selected and shortlisted names from which "Jan Dhan" was picked up for the name of the scheme, the MyGov website said.
Final logo and tagline will be announced soon, the website said.
The Prime Minister had, during the launch of the platform last month, said MyGov platform is a technology-driven medium that would provide this opportunity to contribute towards good governance.