Judicial Protection of Medical Liberty analyzes the recent Supreme Court rulings on COVID-19 restrictions in the much broader context of the Court’s historical medical liberty jurisprudence and lower courts’ vaccination jurisprudence. The Court’s rejection of Jacobson v. Massachusetts as the deferential standard that binds the judiciary in exigent pandemic circumstances when state action infringes constitutional rights has far-reaching implications. The Court’s recent rulings imply that restrictions on individual liberties will be subject to traditional tiers of scrutiny as opposed to deferential review, with or without a pandemic. Medical autonomy lies at the heart of the Liberty Clause and has been fiercely protected by the Court, which at times has deemed it a “fundamental” right and worthy of the strictest judicial scrutiny when infringed by state action. And yet a glaring exception exists for vaccination mandates, which for decades have received no meaningful judicial review by the lower courts. The Court has not issued a meaningful opinion concerning a vaccination mandate since Jacobson in 1905. Vaccination jurisprudence stands alone compared with medical malpractice, products liability, and medical liberty jurisprudence. The enactment of the NCVIA deprives vaccine-injury victims of traditional tort remedies and immunizes vaccine manufacturers – a replacement regime with its own set of constitutional concerns. When combined with the lower courts’ absenteeism relative to vaccination policy, a grave imbalance of power emerged. The nonstop legal battles challenging vaccination laws is a manifestation of this imbalance and will not cease until a separation-of-powers recalibration occurs in vaccination jurisprudence and policy. The importance of a critical analysis of vaccination jurisprudence cannot be overstated. The Article reviews over a century of lower court vaccination jurisprudence and juxtaposes it with Supreme Court medical liberty jurisprudence over the same period to reveal the enormous chasm. Considering the possible forthcoming COVID-19 vaccination mandates and other possible medically invasive mandates, it is time to revisit the lower courts’ vaccination jurisprudence and recognize it as too deferential and constitutionally infirm. Reform is necessary, both to constitutionalize existing vaccination jurisprudence and to set judicial standards of review for forthcoming health mandates. It is yet unclear what standard of review the Court will choose relative to unwanted medically invasive health mandates. On January 25, 2021, the Court vacated the Fifth Circuit’s application of Jacobson to a Texas COVID-19 abortion ban summarily and did not state the proper standard of review. This Article synthesizes the Court’s medical liberty jurisprudence and proposes that all health mandates requiring unwanted medical treatment should be reviewed with a standard of strict scrutiny.