The school beat St Wilfred's of Ripon at Whitby's Turnbull Ground and will now represent the north against the three other regional winners of the county-wide under nines kwik cricket tournament.
The final will be played in conjunction with Yorkshire's 20/20 Cup fixture the same afternoon.
Stakesby had previously seen off competition from Northstead, Gladstone Road and Seamer.
Delighted headteacher Stan Jackson said: "Bearing in mind these are much larger schools, this is no mean achievement and we are incredibly proud of what the children have achieved.
"St Wilfred's are a slightly smaller school than us but have a good cricketing tradition and this is the first time we have entered so we're absolutely amazed.
"We are very grateful to Whitby Cricket Club for their support, not only for allowing us to use their facilities but also our children are attending the junior coaching provided by the club."
Whitby's overseas player, Tasmanian bowler Brendan Godfrey, has also been visiting the school and helping to coach the cricket-mad youngsters.
"It all seems to be coming together for us and it's great news," said Mr Jackson.
"Hopefully we can fly the flag for Whitby – and the northern area.
"The main thing is the children are enjoying it."
Stakesby will get a second trip to Headingley on Friday 18 July and get some coaching from England Cricket Board representatives at the interval of the England v South Africa test match.