Born in Scotland, MacFarlane graduated from the University of Glasgow in 1728 and immigrated to the British colony of Jamaica, where he settled down to a career as a merchant and acquired several sugar plantations operated with slave labour.

In addition to working as a judge and politician, MacFarlane also pursued an amateur career in astronomy in Port Royal and Kingston, using equipment purchased from fellow astronomer Colin Campbell.

[3] At a house he acquired in Port Royal, MacFarlane ordered the construction of an observatory, purchasing astronomy equipment from Colin Campbell, a fellow planter and astronomer who was an acquaintance of Sir Edmond Halley.

Though, as noted by historian David Clarke, MacFarlane's astronomical work was "fairly minimal in modern terms", he was made a fellow by the Royal Society on 20 November 1746.

As he died unmarried, MacFarlane left the majority of his estate in his will and testament to his two brothers, Walter and William; this included the "Serge Island", "Biscany", "Bog Pen", "Glen Goff", "Lennox Castle" and "Windsor" plantations.

In the report, which detailed the university's relationship with slavery and abolitionism, academics Stephen Mullen and Simon Newman noted that MacFarlane's ownership of slaves led to him acquiring a large fortune.