Cotterill, 46, said: "Harry did wonders for this club including winning the FA Cup.
"He asked me to be his assistant at Pompey in 2002 but I felt I was too much of my own man.
"I have known Harry for a long time and he has always helped me in the past.
"I spoke to him on Thursday and he said to go for it. He said Portsmouth was a fantastic club, with great fans and thought I would do well there."