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The former Professional Footballers' Association (PFA) chairman was seriously injured in an incident on the A64 near Bishopthorpe, York, on December 22.
Carlisle, who had spells with the likes of QPR, Leeds United and Burnley during his playing career, is still in hospital at the Leeds General Infirmary, with his wife, Gemma, describing the 35-year-old as "very poorly" but "stable".
A statement from the Metropolitan Police read: "Clarke Carlisle, 35, was charged on Saturday, 20 December with failing to provide a specimen and driving otherwise than in accordance with a licence.
"He is due to appear at Highbury Corner Magistrates' Court on 20 January 2015."
North Yorkshire Police has since opened an investigation into the incident on the A64 and has appealed for witnesses.
