Lijnders will leave Liverpool as assistant manager to take the Salzburg job at the end of the season.
The 41 year-old has agreed a three-year contract and will have Reds coach Vitor Matos as his No2.
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"With Pepijn Lijnders we have been able to win our absolute ideal candidate for the coaching position at FC Red Bull Salzburg," says sporting director Bernhard Seonbucher.
"He is an outstanding football expert and has played a part in a very successful period at FC Liverpool, not least thanks to his qualities in developing players."