The new schools in Woosehill and Winnersh - which are due to be opened in September - will be run by the Glyn Learning Foundation.
The borough council had recommended GEMS Education to the Secretary of State for Education as its preferred education provider, but those plans were rejected.
Cllr Charlotte Haitham Taylor, executive member for children's services, said: "We're excited that GLF Schools is now our partner in this vital programme to lay the foundations to create more quality primary schools in the Wokingham Borough.
"We're sorry that we won't be working with GEMS Education to provide these much needed schools for our borough's children.
"We can assure parents that we are already working closely with GLF Schools and the change should not affect their confidence in the new schools. "Our admissions team is personally contacting all parents who have already expressed their interest in the new schools.
"The two schools will be welcoming their first children from this September. The change in education provider makes absolutely no difference to this."
GLF Schools is a cross phase multi-academy trust based at Glyn School - a secondary school in Surrey - and has said its admissions arrangements will be co-ordinated with, and similar to, Wokingham Borough Council's.
The final admissions arrangements are currently being drawn up.
Jon Chaloner, executive head teacher of GLF Schools, said: "We're thrilled that GLF Schools has been afforded the opportunity to work with Wokingham Borough Council in bringing the two new primary schools to fruition.
"We're confident that our new partnership will enable the schools to open as planned. We look forward to being part of the wider family of schools within Wokingham."
Any parents who wish to express an interest for the new schools should email firstname.lastname@example.org.
An information evening is being held at The Forest School, Robinhood Lane, Winnersh on Wednesday July 10 between 7 and 9pm, where prospective parents can meet the GLF Schools leadership team and find out about the new schools.
To attend the meeting, parents are invited to book their place by emailing email@example.com