Ali Harbi Ali, 25, will appear at Westminster Magistrates’ Court today.
Nick Price, head of the Crown Prosecution Service (CPS) Special Crime and Counter Terrorism Division, 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 CPS reminds all concerned that criminal proceedings against Mr Ali are active and that he has the right to a fair trial.”
Sir David was stabbed while holding a constituency surgery at a church in Leigh-on-Sea, Essex, on Friday.
Police said that despite the efforts of paramedics, he died at the scene.
The 69-year-old was one of Britain’s longest-serving MPs and was married with five children.
Matt Jukes, the head of Counter Terrorism Policing, said: “I want to send my deepest condolences to the family, friends and colleagues of Sir David, who died so tragically last Friday.
“Sir David’s dedication to his family, his constituents and his community, and his positive impact on the lives of so many has shone through.
“Today's charge is a significant milestone in the case, but the work from my colleagues in the Met's Counter Terrorism Command will continue apace.”