At the same time that Jurgen Klopp confirmed his exit from Liverpool in January, his backroom team of Lijnders, Vitor Matos and Peter Krawietz were also revealed to be stepping down from their posts.
Lijnders was briefly tipped as a candidate to succeed Klopp on Merseyside, but the 41-year-old quickly ruled out the prospect of taking the top job as he looked to advance his managerial career elsewhere.
Ajax and Besiktas were among the clubs believed to be interested in hiring Lijnders, but the Dutchman has instead signed a three-year contract with reigning Austrian Bundesliga champions Salzburg.
Lijnders - who succeeds Gerhard Struber, sacked in March - will be joined at the Red Bull outfit by Liverpool colleague Matos, who has also been hired by Salzburg as the 41-year-old's assistant.
Lijnders joining "another beautiful club" after Liverpool
"I'm proud to become the new head coach of FC Red Bull Salzburg and it's a real privilege for me to be here. After PSV Eindhoven, FC Porto and Liverpool, I am joining another beautiful club with a strong structure and an even better academy," Lijnders told the club's website.
"All of the clubs I've been at have been unique, remarkable clubs with a few particular things in common: a one-club mentality where the attack is very important, a true belief to win major trophies and, above all, clubs where passion for the game and ambition to succeed are the base of everything.
"Together with my assistant, Vitor Matos, we will do our best to help the club to grow in a football world that is ever-changing. My family have visited the city before and were overwhelmed by its beauty and by the kindness of the people. This was the final, important step for me to decide to join FC Red Bull Salzburg."
Lijnders's stint at Salzburg will be just his second job as a head coach, having briefly left Liverpool midway through the 2017-18 season to take charge of NEC in his native Netherlands, winning 11 of his 22 games at the helm.
With the Dutchman at the helm, NEC - then a second-tier side - reached the promotion playoffs but were beaten 5-4 on aggregate by Emmen, and Lijnders has also worked as a youth coach at Porto and PSV Eindhoven.
'Pep Lijnders is a real football expert'
Salzburg sporting director Bernhard Seonbuchner talked up Lijnders's work with academy talents as the Liverpool assistant joins a club famed for their development of young players.
"We have been able to get an ideal candidate for the coaching position at FC Red Bull Salzburg in Pepijn Lijnders. He is a real football expert and has been a huge influence on a very successful time for Liverpool with his qualities in developing players," Seonbuchner added.
"The discussions with him were a great success, and there was a clear agreement on the way we want to play, what we are about as a club, and where we want to go together. We are really looking forward to our time with him, but we will do everything we can to take the current season to a successful end first."
Red Bull Salzburg have been crowned Austrian champions in each of the last 10 seasons, but they sit two points behind Sturm Graz at the top of the 2023-24 standings with just one game remaining.
However, Die Roten Bullen are assured of a place in the 2024-25 Champions League third qualifying round at the very least, and they close out their season at home to LASK Linz on Sunday afternoon.