Chairman of the board Ijaz Butt told a media conference in Islamabad that senior batsman Misbah-ul-Haq would lead the team in the two one-day matches against Ireland on May 28 and 30.
"Afridi has been retained as a player in the one-day squad but the captaincy has gone to Misbah," Butt said without elaborating the reason for the decision.
Afridi had captained the team to the World Cup semifinals where they lost to India and recently also guided them to a 3-2 win over the West Indies in the ODI series in the Caribbean.
Afridi ruffled feathers in the PCB and team when he returned from the Caribbean early this month and told the media that he was not happy with people interfering in his work.
Although the all-rounder didn't name names, media reports said he had developed differences with head coach Waqar Younis over team selection issues.
The PCB issued a notice to Afridi to explain his conduct as he had violated the players' code of conduct with his statement on team affairs.
Butt made it clear Afridi had never been given any assurances regarding the captaincy.
He pointed out that the present policy of the board was to appoint captain on a series-to-series basis.
Afridi had struggled with bat and ball in the one-day series in the West Indies but has been leading the national team in limited overs cricket since early 2010 while Misbah has been Test captain since last year.
The national selectors have made no changes in the Test squad playing in the West Indies at present but included Afridi and senior batsman Younis Khan in the side for the Ireland matches.
Younis had returned home before the first Test in the West Indies due to the death of his elder brother.
Pakistan squad: Misbah-ul-Haq (Captain), Younis Khan, Taufiq Umar, Mohammad Hafeez, Asad Shafiq, Azhar Ali, Shahid Afridi, Mohammad Salman,Saeed Ajmal, Abdul Rehman, Umar Akmal, Umar Gul, Wahab Riaz, Junaid Khan, Tanvir Ahmed, Hammad Azam.
