Pete Bailey and Riley Woodman are included, but Jacob Nowell (hamstring) and Dan Bowles (work commitments) are out, while Sam Hutchinson will play for the reserves.
Barometrics defeated Lydney Town Reserves on Saturday in the opening round of the competition, while Whaddon won on penalties at Berkeley Town after a 2-2 draw.
"We're looking forward to testing ourselves against what we expect to be a good physical Whaddon United side," Baros boss Joe Tustain said.
"I'm glad they managed to win the shoot-out in their game on Saturday as it saves us a trip down the M5 during midweek rush hour!
"It's a local derby which players love playing in and hopefully we can continue to make the good progress we feel we have been making in last six weeks.
"It's a cup I would like us to do well in, but ultimately it's another game that gears us up for the league opener."
Barometrics travel to Bibury in Northern Senior League Division One on Saturday.