Farhan recently led Pakistan at the Asian Games in Japan, where they picked up the silver medal after losing in the final to India.
Hasan Nawaz, who scored 96 in the Asian Games final against India, retains his place for the series against Sri Lanka.
Fast bowler Naseem Shah, whose last game in the format came at the T20 World Cup in February, returns to the squad as well for the series that will start in Rawalpindi on Friday.
Shaheen Afridi has retained the captaincy for the ODI series that will follow, with the 50-over squad also welcoming former skipper Babar Azam.
Pakistan T20I squad: Sahibzada Farhan (captain), Abdul Samad, Abrar Ahmed, Arafat Minhas, Fakhar Zaman, Hasan Nawaz, Muhammad Imran Randhawa, Khawaja Nafay (wk), Maaz Sadaqat, Naseem Shah, Razaullah, Saim Ayub, Mohammad Salman Mirza, Shadab Khan, Sufiyan Moqim
Pakistan ODI squad: Shaheen Shah Afridi (captain), Abrar Ahmed, Salman Ali Agha, Arafat Minhas, Babar Azam, Faheem Ashraf, Fakhar Zaman, Muhammad Ghazi Ghori (wk), Haris Rauf, Hasan Nawaz, Naseem Shah, Razaullah, Saad Baig (wk), Saim Ayub, Shadab Khan, Sufiyan Moqim
Arafat Minhas scored a maiden ODI fifty before taking six wickets in one of the great all-round displays to help Pakistan beat England by 87 runs in their tri-series clash in Rawalpindi on Tuesday.
Pakistan pace bowler Haris Rauf is hoping to earn another opportunity in Test cricket as the national side prepare for their next ICC World Test Championship assignment.
Pakistan's disappointing Test series against England has been compounded by an over-rate penalty that will cost them 11 World Test Championship points.
England recovered from a shaky start to beat Pakistan by eight wickets on the fourth day of the third and final Test at Edgbaston, as the home team wrapped up a series clean sweep.
