However, there has not yet been any official reason given for the decision to remove Col Daniel Anrig.
A notice was placed in the Vatican's official newspaper simply stating that he would no longer be serving as commandant.
The Swiss Guard consists of around 110 men and was first formed in 1506.
The force is principally responsible for the Pope's safety and Vatican security.
There is speculation that Col Anrig's deputy, Christoph Graf could be replacing him, who is said to have a more 'paternalistic' style of command.
Roman newspaper, Il Messagero, claims the Pope wants the Swiss Guard to become less rigid and military.
The 77-year-old was photographed breaking protocol by shaking hands with one of the officers back in October.
It's also claimed he told an exhausted soldier he found on guard outside his rooms to 'sit down'.
When the soldier said he couldn't (as it was against orders), the Pontiff was said to have replied "I give the orders around here" and brought him a cappuccino.