The Osaka clash, which has a 6.00am kick-off Irish time, and will be shown as deferred coverage (11.00am) and highlights (6.30pm) on RTE Two, will see McCullough and Wilson, both 23, line out at lock and number 8 respectively.
Munster's Marcus Horan starts at loose head prop for the first time since he played against the US Eagles last November.
In the backs, Ulster wing Tommy Bowe will make his second start in a green jersey following his try-scoring debut against the US.
Leinster full-back Girvan Dempsey offers experience in a back unit which also includes NEC Harlequins utility back Gavin Duffy at outside centre. The Ballina man is set for his first Test start.
Ulster's David Humphreys will captain his country for the third time, having led Ireland against Italy (2002) and Australia (2003) previously, while also extending the caps record for a fly-half to 68.
Commenting on the selection, Niall O'Donovan, who is filling the shoes of Lions-tied Eddie O'Sullivan, said: "The side selected is one which gives us a fresh look to the team, but also has a backbone of experience that is essential at test level.
"Nearly half of the starting 15 have less then ten caps or are new caps, but backing that up we have over 300 caps of experience in key positions."
The former Munster assistant added: "The conditions on Sunday will be a factor in the game, but the quality of training has improved throughout the week as the players have acclimatised to the heat.
"The team was selected to play to a certain game plan and will be prepared for a full-blooded test match."
The Ireland team and replacements to play Japan at Nagai Stadium, Osaka, Japan on Sunday June 12, is as follows:
(15) Girvan Dempsey (Terenure College/Leinster) (14) Tommy Bowe (Belfast Harlequins/Ulster) (13) Gavin Duffy (NEC Harlequins) (12) Kevin Maggs (Belfast Harlequins/Ulster) (11) Anthony Horgan (Cork Constitution/Munster) (10) David Humphreys (Dungannon/Ulster) (Capt) (9) Peter Stringer (Shannon/Munster) (1) Marcus Horan (Shannon/Munster) (2) Frankie Sheahan (Cork Constitution/Munster) (3) Simon Best (Belfast Harlequins/Ulster) (4) Leo Cullen (Leicester Tigers) (5) Matt McCullough (Ballymena/Ulster) (6) Alan Quinlan (Shannon/Munster) (7) Johnny O'Connor (Wasps) (8) Roger Wilson (Belfast Harlequins/Ulster)
(16) Bernard Jackman (Clontarf/Leinster) (17) Reggie Corrigan (Greystones/Leinster) (18) Trevor Hogan (Shannon/Munster) (19) Eric Miller (Terenure College/Leinster) (20) Kieran Campbell (Dungannon/Ulster) (21) Jeremy Staunton (Wasps) (22) David Quinlan (Northampton Saints)
Referee: Nigel Owens (Wales)