David Thomas, 68, of Harding Close, Sutton-On-Sea, was a teacher at Bowl Alley Lane Junior School, now known as Horncastle Primary School, at the time of the alleged incidents.
He is accused of raping and indecently assaulting one child under the age of 12 and indecently assaulting another under 12 between January 1980 and September 1984.
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Thomas is due to appear at Boston Magistrates court on May 11 2021.
Lincolnshire Police have asked any former pupils who wish to speak to the investigating officer to contact 101, quoting incident 50 of April 27 2021.