As a medical student, he began to work as a scientific assistant to the influential free-thinking philosopher and psychologist Alexander Bain (1818–1903), one of the founders of associative psychology.

Around 1860, psychology was finding its scientific foundation mainly in Germany, with the rigorous research of Hermann von Helmholtz (1821–1894), who had trained as a physicist, and of Wilhelm Wundt (1832–1920).

Upon his return to London, the Royal Society sponsored the extension of his stimulation experiments to macaque monkeys, work he undertook at the Brown Institution in Lambeth.

Ferrier had succeeded in demonstrating, in a spectacular manner, that the low intensity faradic stimulation of the cortex in both animal species indicated a rather precise and specific map for motor functions.

These – and other investigations in the same line – resulted in international fame for Ferrier and assured his permanent place as one of the greatest experimental neurologists.

He was also the first physiologist to make an audacious (if scientifically incorrect) transposition of cortical maps obtained in monkeys to the human brain.

A Scottish surgeon, Sir William Macewen (1848–1924), and two English physicians (clinical neurologist Hughes Bennett, and Rickman J. Godlee) demonstrated in 1884, that it was possible to use a precise clinical examination to determine the possible site of a tumor or lesion in the brain, by observing its effects on the side and extension of alterations in motor and sensory functions.

The first one, published in 1876, The Functions of the Brain, describes his experimental results and became very influential in the succeeding years, in such a way that today it is considered one of the classics of neuroscience.

Together with his friends Hughlings Jackson and Crichton-Browne, Ferrier was one of the founders of the journal Brain in 1878, which was dedicated to the interaction between experimental and clinical neurology and is still published today.