The defender passed away in hospital after collapsing during a cup match for Shaw Lane.
Hull have opted to pay their respects by holding a tribute to Wilkinson, who spent time with the Tigers' youth team in his early football career.
Both Hull and Arsenal players will observe a minute's silence before kickoff in Saturday's Premier League match at the KC Stadium.
A statement from Hull read: "He was a popular member of the Tigers' youth team squad that won the Youth Alliance North East Conference title in 2010.
"We ask supporters to join us in remembering Daniel on Saturday during a period of silence, which will start and end on referee Roger East's whistle."
Wilkinson also played for North Ferriby United, Scarborough Athletic, Harrogate Town and Goole Town.