But the Hudoks' attorney, Patrick Lane, said that would deny Olivia her right to a public education, which the county is legally obliged to provide.
Wilfong said her ruling would stand until the West Virginia Supreme Court offers some further guidance.
"Everything with my homebound schooling is going well and I am glad to get to continue that," Olivia Hudok said. "I am very thankful for my family and friends' support. I will continue to stand strong."
Public health officials said allowing her to attend classes without the immunizations could put other children at risk.
West Virginia has some of the nation's strictest limits on exempting children from vaccines required before they can attend school, and some parents have been lobbying the Legislature to change that.
Public health officials, however, warn that the state already suffers low immunization rates against diseases such as polio, whooping cough and measles.
All states, including West Virginia, allow school-bound children to skip immunizations for medical reasons. But while 48 states also permit exemptions on religious grounds, West Virginia and Mississippi do not.