Kosovo Football Federation president Fadil Vokrri said after talks with Bunjaku that they agreed he will leave the post after the end of the qualifiers “to open the way to a newcomer.â€
The team has remaining matches against Ukraine and Iceland next month.
It has only one point in eight matches in Europe Group I, from a 1-1 draw in Finland last year.
Kosovo was accepted by UEFA and FIFA last year, and fast-tracked into 2018 World Cup qualifying.