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Easyjet assumed the fans were being drunk and disorderly when they started singing a song about Quinn when he got on the plane.
The fans were asked to leave the flight and then it was cancelled.
Quinn made sure the supporters were placed in cabs before taking the last cab back himself.
The Sunderland fans were flying from Bristol to Newcastle after see their side beat Cardiff City during the afternoon.
"Myself and members of my staff were on this flight and we vehemently oppose the airline's view that there was disruptive behaviour onboard," said Niall Quinn.
"The mood was humorous and everyone was in good spirits after our fine victory.
"The club was happy to provide transport for the group, which included children, elderly and disabled fans as their safety and well-being was paramount."
Quinn has been generous in the past. He donated around £1m of his tetimonial money to charity in 2002.