The operator agreed to a five-year deal back in 2017, but the company has agreed to an early termination.
The agreement was reached following a review by Everton of its commercial strategy in line with its future growth plans.
A club spokesperson said: "This has been a difficult decision but one that allows us to best deliver on our commercial plan and to grasp the new opportunities now open to us.
"The club would like to thank SportPesa for all the work that has been done together.
"Our partnership has seen our first team visit Africa on two occasions, as well as former players and club staff take part in numerous activations in the region."
SportPesa also has an agreement in place with Championship side Hull City and has previously partnered with Southampton and Arsenal.
Gambling Insider contacted SportPesa for comment, with a spokesperson from the operator saying: "Following the statement released last night by Everton FC, SportPesa can confirm that its commercial arrangement with the club will conclude by mutual agreement at the end of the current season after a successful partnership.
"We would like to thank Everton FC for their support, in particular for their valued input on an array of charitable projects in Africa.
"We understand this agreement allows Everton to pursue a variety of other commercial arrangements for next season, which we note they are already doing."
