In 1794 he became assistant-surgeon in the army, and served in Holland, the West Indies, the Baltic, the Iberian Peninsula, and in the expedition against Guadeloupe in 1815.

[1] Fergusson is widely quoted (though often misspelt) as a source of accounts of the Battle of Copenhagen in 1801, where he was present (as Staff-Surgeon of the troops embarked) with Admiral Lord Nelson on the flagship Elephant, before being entrusted with the conveyance of the British wounded to Yarmouth.

[13] The essay for which Fergusson is most remembered is that on the "marsh poison" theory of malarial infection, reprinted from the Transactions of the Royal Society of Edinburgh January 1820.

He emphasised the fact that malarial fevers often occur on dry and barren soils, either sandy plains or rocky uplands, where rotting vegetation as a cause is out of the question, relying on his own experience with troops in Holland, Portugal, and the West Indies.

[1] But although in his other writings he was possibly the first to correctly suggest insects as vectors of plague, he tantalizingly failed to make the final connection between malaria and mosquitos.