He was elected register of the Order of the Garter on 6 February 1558, and in 1558 was created Doctor of Divinity and appointed prebendary of York and Salisbury.
As the Queen Mary lay dying he was already one of the richest men in England; allowed ten retainers, he was one of the overseers of Cardinal Pole's will.
Boxall was removed from the office of secretary of state by Queen Elizabeth, on her accession, to make way for William Cecil, to whom he acted helpfully.
On 20 July 1569, Boxall, then in custody at Lambeth, wrote to Sir William Cecil requesting leave to visit his mother.
He also wrote an Oration in the Praise of the Kinge of Spaine, left in manuscript in Latin, and probably composed in May or June 1555, on the report of the queen having been delivered of a prince.