Former Nottingham Forest and West Ham forward Harewood, 33, joined Barnsley on a free transfer last summer and scored three goals in 37 appearances for the club.
"Marlon did great for us, he was superb," Flitcroft said. "But he likes being the number one striker at the club and he probably deserves that with what he puts in so it was difficult for him at times to be second target man under Chris O'Grady.
"I think he found that difficult, but Marlon will get something next season no doubt about it due to his form and what he's done in the Championship this season."
O'Grady has returned to parent club Sheffield Wednesday after scoring six goals in 16 appearances for the Tykes during a three-month loan spell that began in January.
Flitcroft added: "Chris was 100 per cent committed to the Barnsley cause and the lads feel like he's one of them.
"Chris feels that, he enjoys playing for us, I know what he needs to get him on the football pitch and he's got a connection with (assistant) Micky (Mellon) and (coach) Martin (Scott) now.
"He feels a part of the family. He became one of the group during our trip to Spain and it was good to see. He's enjoyed his time here, but at the minute he's a Sheffield Wednesday player.
"He's someone we'd love to recruit and we'll be working on that over the next couple of weeks, but while he's a Sheffield Wednesday player all I can say is a massive thank you to Chris for the way he went about his duty."