Patrick Rock, 63, was arrested at his home in London in February after Downing Street contacted police.
The National Crime Agency has charged the ex-Whitehall adviser with three offences of making indecent images of children and one offence of possession of 59 indecent images of children.
The four charges cover offences said to have been committed between July 31 and August 31, 2013.
Asked about the decision at a post-EU summit press conference in Brussels, the Prime Minister said: "I won't be saying anything. It would be purely a matter for the courts and it wouldn't be appropriate to comment."
Rock has been bailed to appear at Westminster Magistrates' Court on July 3.
Judith Reed, a senior lawyer with the Crown Prosecution Service's organised crime division, said: "The decision to prosecute has been taken in accordance with the code for Crown prosecutors.
"We have determined that there is sufficient evidence for a realistic prospect of conviction and that a prosecution is in the public interest.
"May I remind all concerned that Mr Rock has a right to a fair trial. It is extremely important that there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings."
Rock has been charged with three counts of making an indecent photograph of a child and possession of indecent photographs of children.
Rock, a special adviser on policy, was arrested at his home on February 13. He had resigned from his post a day earlier.
He has been an influential figure behind the scenes in the Tory Party for decades, and made three unsuccessful bids to become an MP.
In the 1970s, he was credited with coining the Tory slogan "Cows moo, dogs bark, Labour puts up taxes".
Prior to his arrest and resignation, Rock had been involved in drawing up Government policy on internet porn filters.