Pathan, who was named captain of India Red team, has been replaced by Kerala fast bowler Sandeep Warrier. In Irfan's absence, brother Yusuf Pathan will lead the side.
"Irfan Pathan has been ruled out of the NKP Salve Challenger Trophy, due to injury," BCCI secretary Sanjay Patel said in a statement.
"The All-India Senior Selection Committee has replaced him with Sandeep Warrier in the India Red squad," he added.
A few days ago, BCCI had sent out a statement saying Irfan was ruled out of the ongoing India A-West India A one-day series due to injury.
Challenger Trophy will be played in Indore from September 26 to 29. India Red, India Blue and all-India domestic champions Delhi will feature in the 50-over tournament. India Blue is led by Yuvraj Singh.