He married Rose Elisabeth Paget, who was the daughter of Sir George Edward Paget. Together they had one son, George Paget Thomson, who was Nobel laureate. They also had on daughter, John Paget Thomson.
During his early education he studied in small private schools where he showed great love and talent in science.
In 1870 at age 14, he went to Owens College.
His parents had plans to enroll him as an apprentice engineer at Sharp-Stewart and Company, which was a locomotive manufacture. This never actually happened since his dad died in 1873.
He went to trinity college in 1876. In 1880 he got his BA in mathematics.