The move, announced Wednesday, comes as Southwest faces a $10.2 million civil penalty for continuing to fly nearly 50 planes after the airline told regulators that it had missed required inspections of the planes.
The Federal Aviation Administration, which announced the penalty last week, has also come under fire for failing to immediately ground the Southwest jets when it learned they hadn't been inspected for cracks in the fuselage.
Southwest spokeswoman Christi Day said Wednesday that the move to ground 41 planes resulted in some flights being canceled, although she didn't have a precise figure.
The company said it had 520 Boeing 737 jets at the end of last year. Nearly 200 of them are older models, the Boeing 737-300, that were supposed to undergo extra inspections for cracks in the fuselage.