The 23-year-old lined up in a 60-minute game featuring largely Pompey Academy players at their Copnor Road training ground.
Partnering Ethan Robb in the centre of defence for the bibs, he netted the opening goal from a corner as the fixture finished 4-1 to the opposition.
Whatmough responded with a smile and tongue-in-cheek fist-pump salute to his goalkeeping team-mate and close friend Luke McGee.
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More importantly, it marked his first outing since knee ligament damage against Doncaster in February.
Kenny Jackett had been keen to arrange a fixture to test the centre-half as he continues his return from injury.
As a consequence, the Gosport youngster was pulled out of this morning’s first-team training to feature in the in-house match.
Joining him and McGee in the game were Matt Casey and Josh Flint.
Whatmough was purposely pitted against free-scoring Academy striker Alfie Stanley, a quick mobile player.
And boss Jackett watched second-half developments after first-team training had ended.
Yet Whatmough would finish on the losing side, with Harry Anderson, Charlie Bell, Stanley and Alfie Bridgman scoring in the opposition’s 4-1 victory.