Adnan Rashid said in an open letter to Malala Yousafzai the attack on her was "shocking," NBC News reported Wednesday.
The girl, who was 14 at the time, was shot in October as she rode a school bus to her home in Pakistan's Swat Valley.
Malala survived after the bullet passed through her head and neck and on Friday spoke before the United Nations.
Rashid said he heard of the attack on Malala while in hiding after escaping from a prison where he was being held on charges of planning a failed attack on former Pakistani president Pervez Musharraf.
"When you were attacked it was shocking to me," he said. "I wished it never happened."
Rashid encouraged Malala to return home, but did not apologize for the attack or state whether she "deserved to be killed or not."
"Let's leave it to Allah almighty," he said in the letter. "He is the best judge."