The ministry said William, 29, will be a Royal Air Force search and rescue pilot. He will spend six weeks in February and March at the British outpost, located off the Argentinean coast.
The second in line to the British throne will not undertake any royal duties during his deployment. His wife Kate, formally known as Catherine Duchess of Cambridge, will remain in Britain.
The Falkland Islands are a politically sensitive area. Britain has ruled the area for 180 years, but Argentina claims sovereignty over the islands it calls Las Malvinas.
Next year will be the 30th anniversary of the Falklands War, which claimed the lives of 650 Argentine troops, over 250 British personnel and three islanders.
Britain currently maintains about 1,000 troops in the territory, which is home to approximately 3,000 people.
The Associated Press contributed to this story.