The federal territories (Malay: Wilayah Persekutuan) in Malaysia comprise three territories: Kuala Lumpur, Putrajaya and Labuan, governed directly by the federal government of Malaysia. Kuala Lumpur is the national capital of Malaysia, Putrajaya is the administrative capital, and Labuan is an offshore international financial centre. Kuala Lumpur and Putrajaya are enclaves in the state of Selangor, while Labuan is an island off the coast of Sabah.

The territories fall under the jurisdiction of the Ministry for the Federal Territories, which was formed under Prime Minister Abdullah Ahmad Badawi's administration on 27 March 2006. The first Minister for the Federal Territories was Mohd Isa Abdul Samad. Tengku Adnan Tengku Mansor was the minister from May 2013 to 9 May 2018.

The federal territories were originally part of two states - Selangor and Sabah. Both Kuala Lumpur and Putrajaya were part of Selangor, while Labuan was part of Sabah.

Kuala Lumpur, the state capital of Selangor, became the national capital of the Federation of Malaya (and later Malaysia) in 1948. Since independence in 1957, the federal as well as the Selangor state ruling party had been the Alliance (later the Barisan Nasional). However, in the 1969 elections the Alliance, while retaining control of the federal government, lost its majority in Selangor to the opposition. The same election also resulted in a major race riot in Kuala Lumpur.

It was realised that if Kuala Lumpur remained part of Selangor, clashes between the federal and the Selangor state government might arise when they are controlled by different parties. The solution was to separate Kuala Lumpur from the state and place it under direct federal rule. On 1 February 1974, the Federal Territory of Kuala Lumpur Agreement was signed, and Kuala Lumpur became the first federal territory of Malaysia.

The cession of Kuala Lumpur had the effect of securing the Selangor state government for the Barisan Nasional until the 2008 general election. The separation of Kuala Lumpur meant that Kuala Lumpur voters lost representation in the Selangor State Legislative Assembly and could only vote for representation in the Parliament of Malaysia.

Labuan, an island off coast of mainland Sabah, was chosen by the federal government for development into an offshore financial centre. Labuan became the second federal territory in 1984.

Putrajaya is a planned city, designed to replace Kuala Lumpur as the seat of the federal government. Sultan Salahuddin, who was serving as the Yang di-Pertuan Agong at that time, was asked again to cede land to the federal government. Putrajaya became the third federal territory on 1 February 2001.

In the recent years, efforts were made to forge a common identity for the three federal territories. A flag of Federal Territory was introduced to represent the federal territories as a whole. During the 2006 Sukma Games in Kedah, Kuala Lumpur, Labuan and Putrajaya merged into the unified contingent of Federal Territories.

The official anthem of the territories is "Maju dan Sejahtera", which means "Progress and Prosperity".

Apart from the flag of Federal Territories, each federal territory has its own flag.