John Pat Cunningham, who had a learning disability, was killed by members of an Army patrol in Benburb on June 15, 1974.
The suspect who has been charged is aged 73 and is understood to be a former soldier.
He was arrested in England on Tuesday.
He is due to appear at Omagh Magistrates’ Court this morning.
The murder file was recently reopened by the PSNI’s newly formed Legacy Investigation Branch.