Alexander Simpson (1751-1821) by his second wife Mary, who had helped raise Thomas' cousin Sir George Simpson. He had a half-brother, Aemilius, and a full brother, Alexander. Simpson was a sickly and timid youth, avoiding rough sport. After his father's death the family ended up in financial distress, but despite this he was given a proper education.

Simpson was educated with a view to his becoming a clergyman, and was sent to King's College, Aberdeen,