Wharton, 18, spent time with their EVO-STIK League Premier Division rivals Stalybridge Celtic earlier in the season, and has also been with Colwyn Bay.
He made his senior debut for Tranmere in an EFL Trophy tie at Shrewsbury Town, having been with the club since the age of 16.
The youth loan signing will be available for selection for Saturday's EVO-STIK League Premier Division clash at Nantwich Town.
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