Joan Fraser, who is on a secondment from the Scottish Executive's education department, has been appointed interim chief executive while Youthlink searches for a replacement.
Jaquet's departure coincided with a change of chairman after John Neil stepped down. Former vice-chair Peter McNamara has replaced Neil and will continue until a formal election takes place at Youthlink's annual general meeting in September.
A Youthlink spokesman said Jaquet had not left for another post and wanted to find a new challenge.
Fraser said the changes would not result in major alterations to Youthlink's plans. "The work of the organisation will continue as before," she said. "I don't envisage any major changes."
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