Junaid was struck on the head by a Dhammika Prasad bouncer during the second and final Test and played no further part in the match, which Sri Lanka went on to win by 105 runs in Colombo.
He was hit during Pakistan's first innings, and did not bowl in Sri Lanka's second innings and was absent as Pakistan were bowled out for 165.
Irfan, whose height of more than two metres poses a different challenge to batsman than the shorter Junaid, has played 28 ODIs, the most recent of which was against South Africa in November 2013.
The first match is in Hambantota on 23rd August.
Pakistan ODI squad: Misbah-ul-Haq (captain), Ahmed Shehzad, Anwar Ali, Fawad Alam, Junaid Khan, Mohammad Hafeez, Mohammad Irfan, Mohammad Talha, Saeed Ajmal, Sharjeel Khan, Shahid Afridi, Sohaib Maqsood, Umar Akmal, Wahab Riaz, Younus Khan, Zulfiqar Babar
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