The court ordered the federal appeals court in Richmond, Virginia, to consider the claim by Liberty University in Lynchburg that Mr Obama's proposed healthcare law violates the school's religious freedoms.
A federal district judge rejected Liberty's claims and the 4th US Circuit Court of Appeals ruled the lawsuit was premature and never dealt with the substance of the school's arguments.
The Supreme Court upheld the healthcare law in June.
The justices used lawsuits filed by 26 states and the National Federation of Independent Business to uphold the health care law by a 5-4 vote, then rejected all other pending appeals, including Liberty's.
The school made a new filing with the court over the summer to argue its claims should be fully evaluated in light of the high court decision.
The Obama administration said it did not oppose Liberty's request.
Liberty is challenging both the requirement that most individuals obtain health insurance by 2014 or pay a penalty and a separate provision requiring many employers to offer health insurance to their workers.
The appeals court could ask the Government and the college for new legal briefs to assess the effect of the Supreme Court ruling on Liberty's claims before rendering a decision.
Liberty's case joins dozens of other pending lawsuits over health reform, many involving the requirement that employer insurance plans cover contraception, which are working their way through the federal court system.
The university claims that the healthcare provision forces citizens to fund abortions and contraception, and that this affects religious freedom and the right to conscience.