The move is part of its Debate Europe initiative, through which it aims to engage people with politics at a European level. The commission is offering to co-fund charities to organise citizen consultation projects and debates about the EU and its policies.
Reijo Kemppinen, a representative of the commission in the UK, said charities should approach it with project ideas.
He said the commission would favour those that could continue beyond the funding period, such as setting up networks or educational resources.
"We're not in the business of selling Europe, but we do want to encourage debate about the EU, which is why we need to reach out to the NGOs in the UK - and not just the big ones with offices in Brussels," he said.
Oliver Henman, European and international manager at the NCVO, described Debate Europe as a positive step, but warned that dialogue between the commission and civil society had to be properly structured. He said: "As the commission speaks more to civil society, the relationship has to be more defined, otherwise it will be easy to split up the feedback and forget about it."
He said the NCVO was talking to many of its European equivalents about setting up a European Compact, and added that colleagues in France were lobbying their government, which is set to take over the EU presidency in July.