The typical Atlassian Program Manager salary is $131,321. Program Manager salaries at Atlassian can range from $97,000 - $141,097. This estimate is based upon 3 Atlassian Program Manager salary report(s) provided by employees or estimated based upon statistical methods. When factoring in bonuses and additional compensation, a Program Manager at Atlassian can expect to make an average total pay of $142,265 . See all Program Manager salaries to learn how this stacks up in the market.