On May 10, 2017, President Rodrigo Duterte announced that Cayetano was appointed as Secretary of Foreign Affairs, following the expiration of the one-year appointment ban on losing candidates of the 2016 elections.
Cayetano replaced acting secretary Enrique Manalo, who assumed the post in March 2017 when the Commission on Appointments's (CA) rejected President Duterte's ad interim appointment of Perfecto Yasay Jr. due to the latter's citizenship concerns.

His appointment to the post by President Duterte was approved by the CA's foreign affairs committee on May 17, 2017.
Upon approval of the CA's plenary, he will assume the post as foreign secretary and effectively resign from his post as senator.
On May 18, Cayetano was sworn in by President Duterte at the Malacañang of the South in Davao City.

As Secretary of Foreign Affairs, Cayetano plans an "objective-based" approach in resolving the territorial disputes of the Philippines, which he describes as negotiation through the use of historical facts, such as the Treaty of Paris of 1898 and the United Nations Convention on the Law of the Sea, to defend the Philippines' claims.
He also vowed to avoid "microphone diplomacy", which he describes as the continual issuing of public statements instead of privately negotiating the issues with the parties.

In January 2018, Filipino Congressman Gary Alejano revealed that the Department of Foreign Affairs Secretary Alan Peter Cayetano had approved the Chinese Institute of Oceanology of the Chinese Academy of Sciences to perform a scientific survey of the Rise, while disapproving a French research offer in the Philippine Rise.
Under the agreement, majority of researchers must be Chinese.
On the same month, China told Filipino counterparts that the Philippines has no right in the Philippine Rise.
Filipino President Rodrigo Duterte's trusted spokesperson Harry Roque embraced and defended China's statement, causing outrage from various Filipino sectors.

In March 2018, Cayatano reiterated that the West Philippine Sea is "disputed," despite an international court backed by the United Nations declared that the Philippines has the sole legal right on the resources of the West Philippine Sea which also deemed the Philippines as the internationally acknowledged country with jurisdiction on the area.
Presidential spokesperson Roque also called the area as "disputed," effectively making it as the Duterte administration's policy on the West Philippine Sea.
Acting Supreme Court Chief Justice Antonio Carpio, the main proponent of the West Philippine Sea case, told media that the court ruling is clear and that the Filipino foreign secretary and the presidential spokesperson themselves need to be educated more on the matter, because if they continue to call an undisputed area as disputed, China will use it as leverage against the Philippines.

On October 9, 2018, President Duterte announced that Cayetano had planned to run in the May 2019 elections for the post of representative of Taguig city.
He eventually resigned as Foreign Secretary on October 17, the last day of filing of certificates of candidacies.
He was succeeded by former Permanent Representative of the Philippines to the United Nations Teodoro Locsin Jr as Foreign Secretary on the same day.
On May 10, 2017, President Rodrigo Duterte announced that Cayetano was appointed as Secretary of Foreign Affairs, following the expiration of the one-year appointment ban on losing candidates of the 2016 elections. Cayetano replaced acting secretary Enrique Manalo, who assumed the post in March 2017 when the Commission on Appointments's (CA) rejected President Duterte's ad interim appointment of Perfecto Yasay Jr. due to the latter's citizenship concerns.
His appointment to the post by President Duterte was approved by the CA's foreign affairs committee on May 17, 2017. Upon approval of the CA's plenary, he will assume the post as foreign secretary and effectively resign from his post as senator. On May 18, Cayetano was sworn in by President Duterte at the Malacañang of the South in Davao City.
As Secretary of Foreign Affairs, Cayetano plans an "objective-based" approach in resolving the territorial disputes of the Philippines, which he describes as negotiation through the use of historical facts, such as the Treaty of Paris of 1898 and the United Nations Convention on the Law of the Sea, to defend the Philippines' claims. He also vowed to avoid "microphone diplomacy", which he describes as the continual issuing of public statements instead of privately negotiating the issues with the parties.
In January 2018, Filipino Congressman Gary Alejano revealed that the Department of Foreign Affairs Secretary Alan Peter Cayetano had approved the Chinese Institute of Oceanology of the Chinese Academy of Sciences to perform a scientific survey of the Rise, while disapproving a French research offer in the Philippine Rise. Under the agreement, majority of researchers must be Chinese. On the same month, China told Filipino counterparts that the Philippines has no right in the Philippine Rise. Filipino President Rodrigo Duterte's trusted spokesperson Harry Roque embraced and defended China's statement, causing outrage from various Filipino sectors.
In March 2018, Cayatano reiterated that the West Philippine Sea is "disputed," despite an international court backed by the United Nations declared that the Philippines has the sole legal right on the resources of the West Philippine Sea which also deemed the Philippines as the internationally acknowledged country with jurisdiction on the area. Presidential spokesperson Roque also called the area as "disputed," effectively making it as the Duterte administration's policy on the West Philippine Sea. Acting Supreme Court Chief Justice Antonio Carpio, the main proponent of the West Philippine Sea case, told media that the court ruling is clear and that the Filipino foreign secretary and the presidential spokesperson themselves need to be educated more on the matter, because if they continue to call an undisputed area as disputed, China will use it as leverage against the Philippines.
On October 9, 2018, President Duterte announced that Cayetano had planned to run in the May 2019 elections for the post of representative of Taguig city. He eventually resigned as Foreign Secretary on October 17, the last day of filing of certificates of candidacies. He was succeeded by former Permanent Representative of the Philippines to the United Nations Teodoro Locsin Jr as Foreign Secretary on the same day.
Alan Peter Cayetano