In 1834 he went to study medicine at Edinburgh, and was in his third year appointed assistant to Robert Knox the anatomist, and also to John Reid, the physiologist.
In 1840 Lonsdale returned to Edinburgh and became a partner with his former principal Knox, giving a daily demonstration in anatomy in the class-room and managing the dissecting rooms.
During the epidemic of relapsing fever in Edinburgh in 1843, he had charge of the largest outdoor district, and when his three assistants broke down did the work single-handed.
To the deficiency of vegetable food after the potato blight of 1846, Lonsdale attributed scurvy, then prevailing in a district north of Carlisle; Robert Christison had assigned it to a defective supply of milk.
After his marriage in 1851 he mainly occupied himself in reading, travelling in southern and eastern Europe, interesting himself in Italian art and archæology, and collecting materials for the lives of eminent Cumbrians.
[1] Lonsdale's thesis, An experimental Inquiry into the nature of Hydrocyanic Acid, was printed in the Edinburgh Medical and Surgical Journal for 1839.
At one of the monthly séances of the Royal College of Physicians of Edinburgh he read a paper "On the Terminal Loops of the Nerves in the Brain and Spinal Cord of Man".
Lonsdale married Eliza Indiana, only daughter of John Smith Bond of Rose Hill, near Carlisle, which subsequently became his own residence.