O'Brien, who represents District 17, said he received a $150 scholarship from the IFC last year for his membership in student government.
The IFC scholarship was created last year to increase fraternity involvement in all areas of student government and to assist with his tuition, he said.
"The purpose of the scholarship was not to influence anyone's vote," he said. "As far as I know, no IFC-related issue has come up with Congress in the past two years."
O'Brien will not receive any money this year because of the new bill. O'Brien is president of the IFC.
Speaker Tony Larson proposed the bill Oct. 1 after O'Brien brought the scholarship to his attention. Larson said he does not know of any other Congress member receiving money.
"We don't want people getting paid to be on student government by other organizations," Larson said.
He added that O'Brien's position in Congress is not in jeopardy. "I don't believe it was an ethics violation at the time."
O'Brien said he and Larson wanted to end the practice to prevent possible future wrongdoings.
The bill originally proposed by Larson would have banned all forms of funding, including stipends from student organizations.