Kerrigan picked up a side strain in the defeat at his former club Lancashire last weekend, and misses out in the four-day clash which starts at Wantage Road on Thursday.
Also missing against the Welsh county is seam bowling all-roudner Tom Taylor, which means the County will be without the bowlers who claimed nine wickets between them at Old Trafford.
Coming into the 13 to face Glamorgan are batsman Charlie Thurston, who missed the Lancashire match with a back strain, and pace bowler Jack White.
Overseas signing Wayne Parnell is also included and is in line to make his debut for the club.
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Former skipper Alex Wakely, who missed the trip to Old Trafford for personal reasons, is still absent.
Glamorgan coach Matt Maynard has also named a 13-man squad for the trip to Northampton.
Included is new signing James Harris, who has joined the club on a two-week loan from Middlesex.
Timm van der Gugten has been rested, while in the other change to the squad that lost to Sussex last weekend, Joe Cooke replaces Tom Cullen.
Northamptonshire squad to face Glamorgan: Gareth Berg, Nathan Buck, Ben Curran, Emilio Gay, Rob Keogh, Wayne Parnell, Luke Procter, Adam Rossington, Ben Sanderson, Charlie Thurston, Ricardo Vasconcelos, Jack White, Saif Zaib
Glamorgan squad: Chris Cooke, Andy Balbirnie, Kiran Carlson, Joe Cooke, Dan Douthwaite, James Harris, Michael Hogan, David Lloyd, Billy Root, Nick Selman, Callum Taylor, Roman Walker, James Weighell