Liberty University case "in light of" its own ruling in June to uphold the health insurance mandate at the heart of what critics deride as "Obamacare."
Given that the nation's top court has validated the health care reforms -- after hearing challenges by 26 states opposed to the legislation -- it is considered likely that the appeals court will do the same.
The same appeals court had previously dismissed the Virginia case.
Mat Staver, dean of the Liberty University School of Law, said he was very pleased that the high court had sent the case back to the Fourth Circuit Court of Appeals for another look.
"Today's ruling breathes new life into our challenge to Obamacare. Our fight against Obamacare is far from over," Staver said.
"Congress exceeded its power by forcing every employer to provide federally mandated insurance. But even more shocking is the abortion mandate, which collides with religious freedom and the rights of conscience," Staver argued.
Obama said in February that the government would not require religious organizations to offer free contraception or other services such as abortion on employee health plans, but placed the onus on insurance companies to cover them. The proposed compromise has failed to appease many critics.
The university believes that the constitutionality of the employer mandate is at issue, as well as the government's "forced" funding of abortion, citing the protection of religious freedom afforded by the First Amendment.
The Supreme Court in June dismissed Liberty University's challenge when it upheld the controversial health care law, with chief justice John Roberts casting the decisive vote.
Obama's reforms seek to extend health insurance to another 30 million Americans.
It bars insurance companies from denying coverage to children with pre-existing conditions, allows parents to keep children on their health care plans until age 26, and prohibits lifetime limits on coverage.
Republicans say the reforms will increase costs, cause insurance premiums to rise and hurt the quality of health care.
Despite the worst fears of the Obama administration, the only restriction made by the high court was on the provision to expand coverage to 16 million more poor Americans through the federal Medicaid program.
The court upheld the clause but ordered the government to withdraw its threat to withhold federal funding from states that do not comply.
Monday's ruling could open the door for the health care law to come back before the Supreme Court in 2013, but there is no guarantee that it would agree to re-hear the case.