Thence he migrated to Queen's, where he secured a Michel exhibition, and was placed in the first class of the final classical school at Michaelmas 1826 with the future archdeacon of Taunton, George Anthony Denison, and another.
In 1840, he was appointed, in succession to John Allen Giles, to the scene of his longest and most important labours, the headship of the City of London School.
He treated with conspicuous honesty and fairness the large proportion of boys, not members of the church of England, who from various causes were found there.
He had married, in 1830, to Jane, daughter of Alexander Gordon of Bishopsteignton; and by this lady, who survived him, he left a numerous family.
Besides two sermons, Mortimer published while at Newcastle a pamphlet entitled "The Immediate Abolition of Slavery compatible with the Safety and Prosperity of the Colonies".