Starting July 1, Peter Lee will have a base salary of $333,120 as head of Covered California. The exchange's board granted him a 24% raise in February and it gave Lee another 2.5% increase Thursday.
Covered California's board chairwoman, Diana Dooley, said Lee deserved the additional compensation for his work building the state-run marketplace and his continued commitment to serving consumers statewide.
"We are deeply appreciative of Peter's leadership and we are very happy to recognize his work," Dooley said.
The exchange didn't announce the Feb. 1 raise at the time. A spokeswoman said it was posted on the exchange website May 21 along with salary information for 14 other top managers who all earn more than $100,000 annually.
Lee's $65,000 bonus surpasses the $53,000 bonus the exchange board granted him last year.
Covered California's four-member board also gave a 13% raise to Yolanda Richardson, the exchange's chief deputy executive director. She will make $265,668 starting July 1.
The exchange doesn't draw on the state's general funds. Covered California's primary source of revenue is a $13.95 monthly fee tacked onto every individual policy sold.
Consumer advocates have credited Lee with securing lower-than-expected rates from health insurers the last two years and reaching substantial enrollment of nearly 1.4 million people.
At Thursday's board meeting, Lee cited the exchange's successful outreach to Latinos, its sound financial footing and standardized benefits that make it easier for consumers to compare health plans.
"This is a labor of love for many of us ... to change healthcare in California and to serve as a model for the nation," Lee said. "California can and should feel proud of what we have done to date."
Other state exchanges and their leaders haven't fared so well. Officials in Oregon, Minnesota and Maryland all resigned as troubles mounted during the health-law rollout. This month, Hawaii's exchange began to shut down and shift enrollees to the federal Healthcare.gov marketplace.
Covered California has had its share of operational problems, such as an error-filled provider directory, long call-center wait times and ongoing troubles for policyholders who are transferred to Medi-Cal.
Some observers have also faulted Lee and Covered California for slower growth in year two of open enrollment.
California Insurance Commissioner Dave Jones has repeatedly criticized Lee for a lack of health plan choices in some markets. Health insurers and their 2016 rates will be announced by Covered California next month.