The 41-year-old joined Salzburg in the summer after nine years at Liverpool under former manager Jurgen Klopp and was tipped for success at the Austrian side who are used to challenging for the title each season.
Lijnders helped the Reds win both the Premier League and Champions League along with a plethora of other trophies and was the leading candidate for several roles once he announced he was leaving the club.
The 17-time Austrian champions are fifth in the Austrian Bundesliga, 10 points off league leaders SK Sturm Graz. Salzburg are also 32nd in the 36-team Champions League, with just one win from their six European games.
In a joint statement, Salzburg CEO Stephan Reiter and Managing Director of Sport Rouven Schröder say Lijnders has simply not been up to their standards and are now on the lookout for a new head coach who can revive their disappointing season.
"We began recently to analyse, as planned, what has unfortunately not been a satisfactory season so far. It was clear to see that in many of our matches, we have been far short of our own requirements and aims.
"We have therefore become convinced that our team needs a new impulse under new management, even if we continued to hope for a turnaround until the end. We would like to thank Pep for his work. He put a lot of effort and passion into it and has provided important momentum for our further development.
"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 3 January 2025 with our new coach in place."