Queen Elizabeth concluded a four-day celebration of her anniversary June 5 with a church service and a carriage procession through central London.
The Pope's message, dated May 23 and published by the Vatican June 6, also praised the queen's "personal commitment to cooperation and mutual respect between the followers of different religious traditions."
Pope Benedict said her efforts "contributed in no small measure to improving ecumenical and interreligious relations throughout your realm."
The Pope ended his note offering prayers for the 86-year-old queen's "continuing health and prosperity" and for all the members of Britain's royal family.