As the COVID-19 continues to ravage human population since December 2019, medical professionals and people from other turfs of human knowledge have remained awake, with a view to nipping the spread of the virus in the bud. As early as 30th January 2020, WHO declared the virus a Public Health Emergency of International Concern (PHEIC) and an epidemic, with relentless efforts to arrest its spread. Yet, the virus nibbled away a large fortune in the global economy. While the virus becomes hydra-headed with its variants, vaccines have been developed to curtail its morbidity and mortality. Vaccinations are acknowledged as one of the most important and successful public health interventions. Nonetheless, there are legal hurdles to be crossed as vaccines are deployed to fight COVID-19 across the globe. Consent and fundamental rights of the individuals to be vaccinated sometimes conflict with the public health emergency needs, resulting in mandatory vaccination of every member of a given population. The two sides of the divide have their respective legal backings as inherent in the two locus classicus of Jacobson v. Massachusetts and Schloendorff v. Society of New York Hospital. The former established the principle of mandatory vaccination on account of public health emergency, while the principle of informed consent and self-determination have their roots in the latter. Subsequent cases, including Nigerian decisions in recent years have upheld the principle of informed consent and self-determination in medical treatment. The main thrust of this paper is to examine the effect of corona virus vaccination and COVID-19 status certificate on self-determination and human rights in Nigeria. The paper concludes that with deep rooted trust and transparency, suspicion and mistrust, which are the bedrock of the anti-vaccination movement will fizzle out and the legal conundrum ease off.