He said he will reject any offer of a new contract following his side's disappointing World Cup campaign.
The 38-year-old cited his fractured relationship with some of the players in the national side and the cricket coaching set-up in Pakistan as the reasons for his decision.
"I tried my best but it was difficult. Some guys wanted to learn, but some were not interested at all," Pybus told BBC Sport.
"I won't name any individual but they get to the park and are part of the team but not of the plan.
"They have old habits, they don't want to change. There's a reluctance to learn and change."
Pybus believed there was a role for him in Pakistan cricket but stressed the coaching programme needed a radical overhaul.
"I think I can still contribute to Pakistan cricket, but it is time to move on and let someone else do the job," he added.
"The players worked and trained hard, but they are a product of the Pakistan coaching set-up, and that's what needs to change.
"The players coming into the national team do have talent, but they need to be better prepared, both technically and mentally."
The South African-based Englishman has written a report to the Pakistan Cricket Board on how to improve the structure of the game in the country.
Pybus' relationship with Pakistan first started three years before when he was hired as assistant coach for the 1999 World Cup.
He went on to be promoted as head coach for the tour to Australia that winter, although a 3-0 rout led to him being sacked.
The former Suffolk player was then re-hired for Pakistan's tour of England last year, and helped them pull off a famous last session win at Old Trafford to square the Test series.
His tenure was cut short, however, after he declined to travel to the Asian region following the events of 11 September.
But subsequent poor performances by the team against Australia, and an early exit from the ICC Champions Trophy led to Pybus' selection again.