Williamson's father was a clerk in the East India Company in London. After his retirement in 1840 the family lived on the Continent, where Williamson was educated. He studied at Heidelberg and at Giessen (under Justus von Liebig), where he received his PhD in 1846. He also studied mathematics in Paris. In 1849 he took up the chair of chemistry at London University, a post he occupied until 1887.

Between 1850 and 1856 Williamson showed that alcohol and ether both belong to the water type. Type theory, developed by Charles Gerhardt and Auguste Laurent, was based on the idea that organic compounds are produced by replacing one or more hydrogen atoms of inorganic compounds (which form the types) by radicals. Using the correct formula for alcohol (which he had recently established) Williamson represented the water type as: H₂O (water); C₂H₅OH (alcohol); C₂H₅OC₂H₅ (ether), where the H of water is progressively replaced by C₂H₅.

A further contribution to chemical theory was his demonstration (in 1850) of reversible reactions: two substances, A and B, react to form the products X and Y, which in turn react to produce the original A and B. Under certain conditions the system could be in dynamic equilibrium, when the amount of A and B reacting to form X and Y is equal to the amount of A and B produced by X and Y. He is remembered for what is now known as Williamson's synthesis, a method of making ethers by reacting a sodium alcoholate with a haloalkane.