Glasgow Cathcart MSP James Dornan said he has made the decision with “some regret” to enable him to devote time to launching a campaign to combat sectarianism.
The withdrawal leaves three candidates vying to become Nicola Sturgeon’s second in command - Cabinet Secretary Keith Brown, Inverclyde Council SNP leader Chris McEleny and party member Julie Hepburn, who has worked for a number of senior figures in the party.
Mr Dornan said: “It’s with some regret that I’ve decided to stand down from the race for depute leader of the SNP.
“Over the last few weeks I’ve decided that I want to use whatever energy I have to fight the ongoing curse of sectarianism in Scottish society. I don’t believe I could do both and give them justice.
“I intend to begin to talk to all potential partners in a campaign to change Scotland’s culture towards sectarianism, just as it’s changed its culture towards racism, sexism and homophobia.”
The party is seeking a new depute leader after former MP Angus Robertson quit the role eight months after losing his seat in the 2017 general election.