Upon reading that Quebec may impose a health tax on unvaccinated Canadians, I wondered the following: Prior to COVID-19, had any country fiscally targeted unvaccinated individuals?
Yes, in Jacobson v. Massachusetts (1905) the United States Supreme Court upheld the right of the state to fiscally target unvaccinated individuals. Massachusetts had enacted the following law in relation to the smallpox vaccine:
The board of health of a city or town if, in its opinion, it is necessary for the public health or safety shall require and enforce the vaccination and revaccination of all the inhabitants thereof and shall provide them with the means of free vaccination. Whoever, being over twenty-one years of age and not under guardianship, refuses or neglects to comply with such requirement shall forfeit five dollars.
More recently, in April 2019, the New York City Commissioner of Health issued an emergency order compelling people living within certain zip codes to get the MMR vaccine in response to an outbreak of measles. Non-compliance with this order would be a breach of §3.05 of the New York City Health Code, which is punishable with a minimum fine of $1,000 under §3.11(b). ABC News reported that three people were issued with civil summons for contravening the order.
While not really exactly what your question asks for, I think it's also worth mentioning that there are plenty of examples of parents having tax benefits withheld or being fined if they refuse to get their children vaccinated, e.g. Australia's No Jab, No Pay law, a similar policy in Israel, and even - returning to smallpox - the UK's Vaccination Extension Act 1853 which imposed an initial fine of £1 up to a maximum of £5 on parents who refused to get their children the vaccine.
Australia targeted the parents of unvaccinated children and teenagers by withholding tax credits if they were not immunised according to the national schedule, or on an approved catch-up plan to do so, or with an approved medical exemption.
Wikipedia summarises the 'No Jab No Pay' policy quite well, including its history, arising from decreasing immunisation coverage and highly-publicised infant deaths due to vaccine-preventable disease.
It removed the eligibility for three family- and childcare-related benefits from 2015 and expanded in 2018. One of the benefits is no longer available and one has been "shuffled" back into related benefits, while the third remains. Together they added up to potentially several thousand dollars, depending on family and income circumstances.
I will repost my answer to the very same question on money.stackexchange:
Depends on your definition of "fiscally targeted", but in Slovakia, refusing compulsory vaccination(s) was an offence (priestupok – infraction or misdemeanor, whatever is the correct equivalent) and could be fined up to 331€.
Source (discussing plans to remove the fine and replace it by refusing public school access to unvaccinated children - ironically, the discussion is from the spring of 2019)