The 23-year-old Scottish winger moved to east Lancashire after Cook’s time at the Store First Stadium’s helm but the two will get to work together now after Naismith penned terms on a three-year deal at Fratton Park for an undisclosed fee.
Naismith has made more than 70 appearances and scored 14 goals in two seasons for Accrington after joining them from Glasgow giants Rangers.
Last summer Accrington rebuffed a bid from Bury for Naismith as it did not meet their valuation.
“It’s brilliant to be here,” Naismith told Pompey’s official website.
“I was at a massive club before in Rangers and this place has a similar feel to it. Just walking around gives me a buzz and I can’t wait to move down here properly and get started.
“I knew that the gaffer liked me, so I always had the move at the back of my mind when he took charge.
“For him to bring me to Pompey is a fantastic opportunity and I’m grateful to have been given a chance by such a big club.
“We should be looking for promotion, really, and I’m sure the gaffer will be trying to add to the strong players we’ve already got in order to achieve that.”