The Aft Island for HMS Prince of Wales left BAE Systems' shipyard in Glasgow for the Fife base earlier this month, 10 weeks ahead of schedule.
The section was then taken 1,335 miles around the south of England and up the east of Scotland on a barge to Rosyth.
The ship will now be assembled at the Babcock Rosyth facilities.
HMS Prince of Wales is the second of the new Queen Elizabeth Class aircraft carriers to be built for the UK after the 65,000-tonne HMS Queen Elizabeth.
They are the largest British warships ever constructed and can be used for a range of military activity from war fighting to providing humanitarian aid and disaster relief.
The ships have been constructed in blocks at yards across the UK and are being put together at Rosyth.
They are said to be the first aircraft carriers in the world to use an innovative twin-island design.
The Aft Island is responsible for the ship's mission systems and acts as an aircraft control tower.
The Aircraft Carrier Alliance welcomed the final section of the carrier to the Babcock Rosyth facilities on Sunday morning.
The final 750-tonne section of the Royal Navy's second flagship aircraft carrier has arrived at Rosyth after a journey of more than 1,300 miles.