Dr Rowan Williams' visit is part of the anniversary celebrations and he will tour Portsmouth Naval Base before flying in a Merlin helicopter to the Royal Marines base at Poole, Dorset.
It is his first official Royal Navy visit since his appointment in 2003.
Admiral Nelson led British forces to victory on 21 October 1805, outwitting the French and Spanish forces to win the battle.
Nelson died soon after it ended.
The victory put an end to the threat of Napoleon's armies invading Britain.