Following his arrest, 48 year old Richard Williams from Faversham was suspended from Chilham St Mary's CofE Primary School, and he later resigned.
A spokesman at Kent Police said: "Richard Williams, 48, from Alexander Drive in Faversham, has been charged with possession of indecent images. He is due to appear at Canterbury Magistrates' Court on Friday April 28 2017."
The allegations have reportedly shocked the village school, which was rated 'Good' by inspectors from Ofsted after their most recent visit, in 2013.
A Kent County Council (KCC) spokesman said: "The whole school community was very distressed to hear of Mr Williams's arrest on suspicion of possessing indecent images of children, and that he had been charged with this offence.
"As soon as the chair of governors was informed of Mr Williams's arrest, immediate action was taken to safeguard the school's pupils.
"Mr Williams was suspended, prevented from entering the school site and, following a meeting with the chair of governors and KCC's area education officer, he resigned with immediate effect."
Police have found no evidence to suggest any child connected with Mr Williams has been affected, according to council officials.
The spokesman went on to say no parent, pupil or member of staff had come forward to complain about Williams's behaviour towards children.