EEF specialises in running randomised control trials to deliver research into improving attainment in early years. But it said it has often had to turn down funding applications from early years providers as the projects they propose are too small-scale.
It usually requires research programmes spread across 50 to 100 nurseries or settings to produce viable results.
The Nuffield Foundation said it will address this problem by acting as a "supporting pipeline", helping early years organisations to develop early-stage projects into large-scale trials suitable for EEF support.
The amount of funding available is currently undecided as investment will depend upon the applications the organisations receive.
EEF chief executive Kevin Collins said more research was required in early years as "there is less strong evidence to indicate which specific interventions are most effective in improving children's learning and development".
EEF currently funds seven trials in early years, involving about 9,000 schools and nurseries, but Collins said there were "lots of good ideas out there which need some development support first".
"Our new partnership with the Nuffield Foundation aims to create just such a pipeline, to build the evidence base of ‘what works' in the early years.
"It will enable organisations with innovative ideas to test and learn, giving them the support they need to put together strong applications for EEF trial funding."
Nuffield Foundation director Josh Hillman said the partnership would mean more children will benefit from approaches that are proven to improve outcomes.
Applications for funding close on 4 September 2017. The organisations expect to commence work on chosen projects from January 2018, and to publish the first results between a year and two years later, depending on the scale of the programmes.