Prince Charles will represent her at the summit, which will take place in Sri Lanka in November, the BBC said.
Buckingham Palace said it was reviewing how much the queen travels.
The queen, 87, is the head of the Commonwealth, and every two years all Commonwealth leaders meet to discuss global issues.
The queen first attended the Commonwealth meeting in Ottawa, Canada in 1973 and has been at every one since.
Prince Charles will be performing one of his most significant duties to date by stepping in for the queen, the BBC reported.
The decision comes amid controversy surrounding the location choice for the meeting. Campaigners are asking for an investigation of human rights abuses during the Sri Lankan civil war before a meeting takes place.
Britain is facing pressure to lead a boycott of the meeting, the BBC said, but Buckingham Palace said the queen's decision was not related to the protests.