The famous singer, whose bid to become joint-owner of the club failed in 2014, won the competition and helped design the new shirt with his grandfather Len.
The League One club revealed that Tomlinson's design was among five top entries, which went to a public vote and the boyband member received around a third of the votes.
Tomlinson told the club's official website: "I designed the kit with my granddad when I was home a few weeks ago. We used to go to Belle Vue together, so it has always been a family affair with us and to now have a hand in next season's away shirt is brilliant. I can't wait to see my team wearing it."
While some fans opted to congratulate the singer on Twitter, others branded the result a fix, which prompted the club to release a statement confirming that the process was "fair".
A spokesperson told the club's official website: "The process for receiving kit designs, shortlisting and the public voting for our kit design competition followed strict legal guidance to ensure that the club adhered to competition law and that all processes were fair.
"We are aware that the result of the competition has attracted some mixed feedback, but we can assure our fans that the voting process for the 2016-17 shirt designs was all was fair and above board."