Lijnders, the former Liverpool assistant coach, was appointed Salzburg coach in May.
Despite his side winning two of the last three league games, including a 3-0 win over Austria Klagenfurt on Saturday, Salzburg chose to part ways with the Dutchman
"During the six months under Pepijn Lijnders, our qualification for the Champions League was a plus," the club said in a statement.
"After the successful start to the season, there have been many unsatisfactory performances, however, which have led to RB Salzburg being ten points off the top of the Bundesliga."
"We are now very intensively looking for a new coach and will communicate as soon as a decision is made. We clearly want to start training again on January 3rd with our new coach in place."