Lieutenant Commander Rod Strathern is now at the helm of Nelson’s flagship, famous for its role in the Battle of Trafalgar and for being where the UK’s most famous admiral died in 1805.
Lt Cdr Strathern, 46, who has a deep interest in military history, said he was honoured to be selected for the position.
The father-of-two, from Winchester, Hampshire, said: “Command of HMS Victory is a huge privilege for any CO but to be the 100th adds a particular significance and I am conscious that I am following in some very illustrious footsteps.
“HMS Victory is a priceless national treasure and I intend to ensure she is well looked after.”
Saying farewell as CO, and to the Royal Navy, was Lieutenant Commander DJ “Oscar” Whild, 50, who took command of HMS Victory in September 2008.
The father-of-three from Ports- mouth, who is retiring to France, said: “Being in command of HMS Victory for the past three years has been a great honour for me.
“The ship certainly gets under your skin and, although it is time for me to move on, it will still be a wrench to let her go.”
HMS Victory was launched in 1765 at Chatham Dockyard and was commissioned into the Royal Navy in 1778.
It is undergoing a £16m five-year refurbishment and repairs programme, which is being carried out by BAE Systems.