The Conservative MP for Southend West was fatally stabbed on Friday during a constituency surgery in Leigh-on-Sea in Essex.
Ali Harbi Ali, 25, from London, has been charged with murder and preparing acts of terrorism, the Crown Prosecution Service said.
He is due to appear at Westminster Magistrates’ Court on Thursday afternoon.
Nick Price, of the CPS, said: “We will submit to the court that this murder has a terrorist connection, namely that it had both religious and ideological motivations.
He has also been charged with the preparation of terrorist acts. This follows a review of the evidence gathered by the Metropolitan Police in its investigation.
“The Crown Prosecution Service reminds all concerned that criminal proceedings against Mr Ali are active and that he has a right to a fair trial.”
On Monday, Parliament paid tribute to Sir David as it was announced that Southend would be granted city status, in recognition of his decades-long campaign for the seaside town to be given the honour.