The child was airlifted to Swansea's Morriston Hospital following the incident on Telelkebir Road in Hopkinstown, Pontypridd, on Tuesday.
He was in a stable condition after suffering serious leg injuries.
The man charged in connection with the incident will appear at Merthyr Tydfil Magistrates' Court on Thursday.
A 20-year-old man has been charged following a collision between a quad bike and a seven-year-old boy in Rhondda Cynon Taff.