Barroso, one-time Conservative prime minister of Portugal, told reporters at a press conference on Tuesday that he had accepted a request to run for another term at the top of the body charged with regulating and proposing EU legislation.
He said he was "honoured that the President of the European Council has today asked me if he can put forward my name for a second mandate," adding that he had agreed to the request.
The Commission chief made his announcement on the back of talks with leaders from Sweden and the Czech Republic, which currently holds the rotating EU presidency.
Czech Premier, Jan Fischer, said Barroso had approved his plan to seek backing from other countries ahead of a summit of all 27 national leaders in Brussels next week.
Some member states have said they want the new Commission president to be named during the upcoming summit. The positive results for centre-right parties in EU elections are likely to boost Barroso's bid.
Barroso, who has held the post since late 2004, is the only official candidate so far.