Sinclair retired on a pension to Scotland and also spent time in Europe. He held discussions on scientific issues with Charles Darwin, Thomas Henry Huxley and Richard Owen. He became a fellow of the Linnean Society in 1857. He returned to New Zealand in 1859 to collect in the South Island and on Stewart Island material for a supplement to Hooker's Handbook of the New Zealand flora. He made arrangements with Sir Julius von Haast to explore Mount Cook, but was drowned on 26 March 1861 endeavouring to cross the flooded Rangitata River. Richard Stringer and Sinclair had one horse between them. Their plan was to ride the horse through the river and send the horse back to the second man. Sinclair rode to an island in the middle of the river and tried to send the horse back, but it carried on to the opposite side. Sinclair swam after it, but drowned. He was buried at Samuel Butler's Mesopotamia Station nearby. Sinclair had never married.