The internal structure of Capel Aberfan, built in 1876, was destroyed and four homes were evacuated after the blaze in the early hours of Saturday.
The chapel was used as a temporary mortuary following the Aberfan mining disaster in 1966 and housed a memorial organ.
Daniel Brown, 26, will appear at Merthyr Crown Court on 28 July.
A man has been charged with arson with intent following a fire which gutted a historic chapel in Merthyr Tydfil.