The 32-year-old, who has played 354 one-day internationals, was the only senior player overlooked for the tournament with chief selector Iqbal Qasim saying Afridi's bowling had cost him his place in the squad.
"Afridi's bowling has not been up to the mark in recent matches," he said in a news conference on Monday.
"He has not taken wickets and his primary role in the team is that of a bowler."
Afridi failed to take a wicket in the recent one-day series against India and South Africa.
Selectors recalled middle order batsman Umar Amin and included five pace bowlers for the tournament.
The young attack includes uncapped youngster Asad Ali as well as Ehsan Adil, Junaid Khan, Wahab Riaz and Mohammad Irfan.
Qasim said senior players Kamran Akmal and Shoaib Malik needed to impress.
"Both need to contribute significantly to the team's performance because in recent matches they have not lived up to our expectations," he said.
Pakistan will play a one-day series in Scotland and Ireland in May before going to England for the Champions Trophy in which they are in a group with South Africa, India and West Indies.
It will be their first visit to England since the 2010 spot fixing scandal.
Pakistan squad: Nasir Jamshed, Imran Farhat, Mohammad Hafeez, Asad Shafiq, Misbah-ul-Haq (Capt), Shoaib Malik, Umar Amin, Kamran Akmal, Saeed Ajmal, Abdul Rehman, Junaid Khan, Mohammad Irfan, Asad Ali, Ehsan Adil and Wahab Riaz.
- Sports & Recreation
- Junaid Khan
- Umar Amin