In 1960, while Syria was part of the United Arab Republic (UAR), retired colonel Pullong Arpa of Sulu was appointed by President Carlos P. Garcia as the first Philippine ambassador to the country.

[1][2] Although Syria left the UAR the following year as a result of the 1961 Syrian coup d'état, the Cairo mission continued to exercise jurisdiction over the country.

[13] On January 24, 2021, The Washington Post broke a story accusing Embassy officials of mistreating and abusing female Overseas Filipino Workers (OFWs), many of whom were trafficked into the country illegally, who were in their care.

[18] On August 30, 2011, after Arroyo was succeeded as President by Benigno Aquino III, Cuyugan was controversially recalled by the Department of Foreign Affairs (DFA) and replaced with chargé d'affaires Ricardo Endaya.

DFA spokesperson Raul Hernandez disclosed to the media that because the mission's focus has shifted to evacuating Filipinos from Syria, Cuyugan was replaced by Foreign Affairs Secretary Albert del Rosario with a diplomat with more experience in repatriation,[18] although the DFA was also reportedly incensed by Cuyugan's position that Filipinos in Syria were safe despite the deteriorating security situation there,[19] reinforced by a statement he made to the media to that effect.