The 21-year-old has made five senior appearances for the Premier League club, which all came during the 2018-19 campaign.
The England Under-20 international had a stint on loan at Dutch club De Graafschap last year.
He joins fellow Saints team-mates Tom O'Connor and Tyreke Johnson on loan at MEMS Priestfield Stadium.
"Callum is very highly thought of at Southampton and he is here to further his education," Gills boss Steve Evans told the club website.
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