The partnership will create a new fund to help transport groups buy their own vehicles once they have secured government contracts.
A local transport bill was announced in last week's Queen's Speech. It includes proposals to encourage the use of community transport organisations and would allow community groups to employ paid drivers rather than depend on volunteers.
The fund will be able to provide finance in the form of loans or support for leasing office space. No exact figure has been set, but Big Issue Invest said that it would provide as much finance as is needed to meet demand from community organisations.
"Being able to offer members further funding solutions will be an immense boost to improving the sustainability of local public services for the most disadvantaged people in society," said Keith Halstead, chief executive of the Community Transport Association.
Nigel Kershaw, chief executive of Big Issue Invest, said that it would be a "dynamic and effective partnership", and that the fund would be designed to meet the specific needs of community transport groups.
"Leasing vehicles is completely different from buying buildings or providing working capital," Kershaw said. "Having a partnership between a social enterprise investor and a social enterprise association is a really good structure for the future."