Matt Clarke will join Pompey from Ipswich in a permanent deal on July 1, with Adam Webster moving in the opposite direction.
The 19-year-old centre-back has agreed a three-year deal with the Blues, who will also receive an undisclosed fee.
Clarke spent the 2015/16 campaign on loan at Fratton Park, scoring once in 33 appearances and is excited about returning.
“I’m over the moon,” he said. “It was a good season for me on a personal level, although we didn’t quite hit the heights we were aiming for.
“I’ve come on leaps and bounds – playing under-21 football just isn’t the same as turning out in front of massive crowds at Fratton Park.
“It was devastating for me to miss the play-off games with a niggly injury after working so hard throughout the campaign.
“But now I’m raring to get started again and am looking forward to what’s ahead at Pompey.
“This club might be in League Two, but everything’s set-up for us to be at a higher level and we want to make sure that happens.”
Webster scored five goals in 81 appearances after graduating from Pompey’s academy and represented England at under-19 level.