The announcement was followed by speculation that Younis himself had decided to quit the position as he was not happy with his role and wanted greater say in selection matters.
According to a source, he was not satisfied with the way the national team is being prepared for the future.
Younis was appointed last year in November on a two-year contract until the 2022 ICC T20 World Cup.
PCB Chief Executive Wasim Khan said it was sad to lose an expert of the stature and experience of Younis.
"Following a series of discussions, we both have reluctantly but mutually and amicably agreed that it was time to move in different directions," he added.
"...hope he will remain available to assist the PCB by sharing his vast knowledge with the emerging cricketers."
Both PCB and Younis have agreed to not to make any further comment on the reasons for the former captain's departure, the Board statement said.
Younis, who remains Pakistan's top Test run-getter with over 10,000 runs, has had his fair share of problems with the cricket establishment.