On 28 May 1847 Chalmers returned to his house at Church Hill in Morningside, near Edinburgh, from a journey to London on the subject of national education. On the following day (Saturday) he was employed in preparing a report to the General Assembly of the Free Church, then sitting. On Sunday, the 30th, he continued in his usual health and spirits, and retired to rest with the intention of rising at an early hour to finish his report. The next morning he did not make his appearance, and he was discovered lying dead in bed.
Chalmers was interred in the Grange Cemetery on 4 June, the very first burial in that cemetery. His grave is on the north wall, near the north-west access. A large crowd of persons of all denominations accompanied his remains to the grave.