In 1861 Baker became an assistant to the consulting engineer John Fowler (Fowler, Sir John, 1st Baronet) and by 1875 was his partner. Baker became Fowler's chief assistant in 1869 and as such was responsible for the construction of the subterranean District Railway from Westminster (Westminster, City of) to the City of London (London, City of). He also served as consultant for the building of other London Underground lines, all bored deep in the London clay. His other projects included the docks at Avonmouth and Hull and the ocean transport (1878) of the 180-ton obelisk Cleopatra's Needle from Egypt and its reerection in London.

In 1867 Baker wrote a series of articles, “Long Span Bridges,” discussing the application of cantilevers, which were later used in his Forth Bridge (1882–90). At the completion of that bridge, Baker was knighted. He served on numerous government commissions and boards and, among other assignments as a consultant, implemented William Willcocks (Willcocks, Sir William)'s plans for the Aswān Dam (1898–1902). In the United States he was consulted by James B. Eads (Eads, James B.) on the construction of his steel bridge over the Mississippi River at St. Louis, Missouri, and, when the first Hudson River tunnel threatened to fail, Baker was called in to design a tunneling shield that allowed work to be completed. Baker was president of the Institution of Civil Engineers in 1895–96 and a vice president of the Royal Society from 1896 to his death in 1907.