The charity, which works with disadvantaged young women in England and Wales, is conducting the exercise with all of its 280 employees.
Those who are put in lower pay brackets will see their current salaries protected for two years before the new arrangements begin. Most salaries are expected to remain the same and some will increase, the charity said.
A spokeswoman for the YWCA said the process was being conducted to ensure that salaries were consistent. "The decision to conduct a job evaluation came after requests from staff who felt there were some discrepancies in the current salary structure," she said.
"The process is being conducted with the full cooperation of the trade union and with total transparency."