David Thomas, 68, from Harding Close, Sutton on Sea, has been charged with four offences under the Sexual Offences Act 1956.
A Lincolnshire Police spokesman said: “The charges relate to rape and indecent assaults on victims under the age of 12 years between January 1980 and September 1984.
“The offences relate to a period when Thomas was employed at Bowl Alley Lane Junior School, now known as Horncastle Primary School.
“If there are any former pupils that would like to speak to the investigating officer, please contact Lincolnshire Police on 101 quoting incident 50 of April 27.”
The defendant is due to appear at Boston Magistrates’ Court on May 11.