When he reached 19 in Abu Dhabi he overtook Javed Miandad's mark of 8,832, which has stood since 1993.
Younus, 37, is playing in his 102nd Test having made his debut in 2000.
He is now the 15th highest run scorer in Test history, and third among active players, behind only Shiv Chanderpaul and Alastair Cook.
Younus reached the record in style, hitting a six over deep mid-wicket off Moeen Ali to go past Miandad.
He eventually made 38 before being caught at short mid-on by Cook off the bowling of Stuart Broad as Pakistan established a strong position on the first day after winning the toss, with Mohammad Hafeez compiling 98.
Pakistan batsman Younus Khan has become his country's all-time leading Test run scorer on the first day of the first Test against England.