Staff members at Many Rivers Counselling Services have ratified a tentative agreement, after 36 hours at the bargaining table.
Its union said the deal resolves all outstanding issues, including flex time which was the main stumbling block.
"We have arrived at a situation where the number of hours of flex time that we have agreed to is - allows flexibility of the counselors and the staff to provide the services and there is a provision for some control by the employer to pre- approve over a certain number of hours," said Steve Geick, the president of the Yukon Employees Union.
Eighteen staff with Many Rivers were on the picket line for three weeks.
They will return to work Friday.
Many Rivers provides counselling services in Whitehorse, Watson Lake, Dawson City and Haines Junction.