He succeeded the Queen as patron of the Rugby Football League in 2016.
Simon Johnson, interim chair of the RFL, said: “The Challenge Cup final is established as a special and historic day in the British sporting calendar.
“We hope His Royal Highness will enjoy seeing the two current best teams at Rugby league’s showpiece event.”
St Helens and Warrington are the top two teams in the Super League table, with Saints already confirmed as League Leaders’ Shield winners.
‘A return to tradition’
Dave Woods, BBC Rugby league correspondent
The 118th Challenge Cup final will be a first, in that it is the first time that Warrington and St Helens have met in the competition’s final.
But Prince Harry presenting the trophy is a return to tradition. His great grandmother, the Queen Mother, handed over Rugby league’s oldest trophy in 1980 to Hull Kingston Rovers’ winning captain Roger Millward, and the Duke of Edinburgh was guest of honour at the 1995 final – the last of Wigan’s eight successive Challenge Cup final victories.
The first royal to present the trophy was Edward VIII, then Prince of Wales, in 1933. King George VI was at Wembley in 1948 to see Wigan against Bradford.
The Queen has been in attendance twice; for the 1960 final between Hull and Wakefield, and in 1967 when Featherstone beat Barrow.
Other notable guests of honour have included prime ministers Clement Attlee, Harold Wilson, Margaret Thatcher and Tony Blair.
In more recent years stars from other sports, such as Olympic gold medal-winning rower Sir Steve Redgrave, and heroes from within Rugby league, including the late Steve Prescott in 2010, have performed the duty.
As the first major royal chief guest in nearly 25 years, Prince Harry is also expected to meet with the winners of this year’s women’s and wheelchair Challenge Cup finals before the men’s game.