Thomson was born around 1619, and served under Prince Maurice in the English Civil War; he was taken prisoner by the parliamentarians at Newbury in 1644 and spent a period in Fleet prison in London. On his release he attempted to obtain a license from the "College of Physicians", but finding the licensing charge too excessive, went on to obtain his M.D. from Leyden University (in the Netherlands) instead, graduating on 15 June 1648; the thesis he submitted for this purpose was "Disputatio de Apoplexia" (Leyden, 1648). He subsequently rejected Galenic medicine, becoming a strong supporter of the ideas of Jan Baptist van Helmont (Helmontian medicine).