After his initial apprenticeship as a lithographic writer and engraver at the Fife Herald in Cupar, he moved to Glasgow in 1849 and worked as a lithographer and engraver for Joseph Swan until 1855.
Thomas Annan set up business with George Berwick at 40 Woodlands Road, Glasgow, listing in the 1855 - 1856 Glasgow post office directory as calotypists, practitioners of this early form of photography. In 1855, he photographed the ship RMS Persia, under construction on the Clyde, which was probably a commission by engineer, Robert Napier. This photograph was part of a group of images sent to the Photographic Exhibition in connection with the British Association.
After dissolving his previous partnership, Thomas Annan established himself in a photographic studio at 116 Sauchiehall Street during 1857. In 1859, the business moved to 200 Hope Street and he was also able to establish a printing works in Hamilton in 1863. First interested largely in architectural photography and then portraits, as well as photographing artworks and maps, in 1866 Annan photographed slum areas of the city. These images were used by Glasgow City Improvement Trust to document the overcrowded, unhygienic conditions ahead of extensive redevelopments. It was this series of photographs, created between 1868 and 1871, entitled Old Closes and Streets of Glasgow, that ensured his prosperity.
In 1869, Annan purchased the contents of Rock House, which belonged David Octavius Hill, which included many of Hill's photographs and negatives. These were eventually exhibited by Thomas' son, James Craig Annan, and reproduced in photogravure in Alfred Stieglitz's journal Camera Work.