He entered the University of Edinburgh in 1803, and studied under his father's friend Dugald Stewart, and for a time was expected to follow a career in philosophy rather than medicine.

Struck by the poverty he encountered, Alison advocated poor relief in Scotland be extended from the sick and infirm to include the healthy impoverished.

He argued that poverty arose from social factors, not sin and sloth, and that higher wages should be paid to workers to mitigate disease by reducing the effect of overcrowding and destitution.

In his 1840 publication Observations on the management of the poor in Scotland and its effect on the health in the great towns, Alison argued that the government and its agencies had a major role in the alleviation of poverty and that this undertaking should not be left to religious groups or private charities.

Alison counter argued, saying that it was unrelieved poverty that truly lowered the morality of the poor, and not providing any relief not only made the impoverished more prone to contract disease, but also more short-sighted and reckless.

There was also no evidence in Alison's mind that the English system of governmental relief had brought any of the negative consequences that the Scottish had attributed to it, and rather “the English people receive a temporal reward for their more humane and merciful management of the poor, in the comparative exemption of most of their great towns from the curse of contagious fever.” Alison also promoted preventive social medicine and initiated a program to vaccinate children against smallpox, and he established Edinburgh's Fever Board to combat epidemics.

He advocated speedy diagnosis of the ill and, where found to be contagious or infectious, he recommended fumigation and ventilation of the residence and prompt hospitalisation for the patient.

In strongly advocating government intervention to alleviate poverty as a means to combat disease, Alison was ahead of his time but he lived to see public opinion move closer to his initiatives.