The new director, Graeme Brown, will relocate from his current post as director of communications, policy and campaigns at Shelter England.
Stoddart announced his resignation in March, during the height of staff strike action against Shelter over new, longer working hours and an end to incremental pay increases. However, he said at the time that his departure was not related to the management dispute (Third Sector Online, 11 March).
Brown, who is originally from Glasgow, has previously worked at the Children's Society, the Home Office, and the Cabinet Office. He is due to take up his post on 21 July.
"I look forward to leading Shelter Scotland at this critical time for housing and homelessness," he said.
Denis Robertson Sullivan, chair of the Shelter Scotland Committee, said: "We are pleased that Shelter Scotland has been able to attract back to Scotland one of our most senior UK managers.
"Graeme will be a powerful and highly informed advocate for good housing in Scotland."