He said he is leaving "after prayerful consideration to protect the organization and to help the healing in the local theatergoing and creative community."
Eckern said he "chose to act upon my belief that the traditional definition of marriage should be preserved" but had no idea his contribution would generate such controversy. He said his sister is a lesbian in a domestic partnership, which he understands to carry the same legal rights as marriage.
The boycott calls - led by artists including "Hairspray" composer Marc Shaiman - began after activists learned Eckern contributed $1,000 to the Yes on 8 campaign. Last week, voters approved Proposition 8, which changes the constitution to ban same-sex marriage.
Lisa West, regional spokeswoman for the Church of Jesus Christ of Latter-day Saints, said Eckern is a member "in very good standing" and the Mormon church supports his decision to resign.
Fred Karger, the founder of Californians Against Hate, which was created to publicize donors to the Yes on Proposition 8 campaign, said he was not involved in the theater boycott effort and was saddened that Eckern resigned.
"That's not good news, but there's going to be a lot of fallout from this (gay marriage ban)," Karger said. "Of course, a lot of lives were ruined on the other side."
He said his Web site has received thousands of visits from those tracking Yes on 8 contributors.
Ron Prentice, chairman of the Yes on 8 campaign, issued a statement criticizing gay marriage supporters who "cherish tolerance and civil rights (but) are unabashedly trampling on the rights of others."
The theater company, Sacramento's oldest arts organization, said it is not involved in political issues but doesn't interfere with employees' rights to express their views. The company issued a statement thanking Eckern for his 25 years of service.
Eckern was the company's chief operating officer and its artistic director since 2002. The company produces Sacramento's annual Music Circus and plays at Broadway Sacramento and the newly opened Cosmopolitan Cabaret.