The earliest contacts between the peoples of the Philippines and Cambodia may date as far back as the 6th century.
In the Spanish colonial era that followed centuries later, historical records of Spanish attempts to intervene in Cochin China in the 16th century describe Spanish expeditions out of Manila that may have included Filipino contingents. However, Spanish exploits in supporting the Kingdom of Cambodia against the more powerful Kingdom of Siam ended after the massacre of the Spanish garrison in Phnom Penh.
Contacts were again re-established in the 19th century when the Spanish Crown agreed to assist the French in Indochina.  Filipinos forces mustered by the Spanish in Manila were brought to Indochina and placed under French command.  The Filipino forces were critical in efforts to storm and capture the Vietnamese cities of Tourane (present-day Danang) in 30 August 1858 and also in the capture of Saigon (present-day Ho Chi Minh City) on 17 February 1859.
When Cambodia became a French protectorate, some of the Filipino troops were transferred to Cambodia and assigned as palace guards and cannoneers for King Norodom I.
King Norodom I visited Manila in 1872 as part of a goodwill tour of several countries.  Before ending his Philippine visit, he made arrangements to bring back to Phnom Penh a group of Filipino musicians to form the Royal Brass and Reed Band.  When he returned to Phnom Penh, he promoted the officers of his Tagalog militia.
The Filipino militia and musicians settled in Phnom Penh and outlying areas and married into Khmer and Vietnamese families.
Gen. Sosthène Fernandez, the son of one of the Filipino musicians, became a police chief and, later, a prominent politician in Cambodia.  After Prince Norodom Sihanouk was deposed in 1970, Pres. Lon Nol appointed Gen. Fernandez as the Commander-in-Chief of the Khmer National Armed Forces (Force Armée Nationale Khmère or FANK).
In more contemporary times, Filipinos were commissioned as peacekeepers for the United Nations Transitional Authority in Cambodia (UNTAC) from 1992 to 1993.
Official diplomatic relations between the Philippines and Cambodia were established on 20 August 1957. Between 1958 and 1965, Philippine interests in Cambodia were overseen and managed by the Philippine Embassy in Saigon, Vietnam and, at some point, by the Philippine Embassy in Bangkok. 
The first resident diplomatic mission in Cambodia was established in 1965 with the late Senator and renowned actor Rogelio de la Rosa as first Philippine Ambassador from 1965 to 1971, during which he developed close official and personal ties with the late King Father Norodom Sihanouk.
On 18 March 1975, the Philippine Government closed the Embassy in Phnom Penh when the defeat of the Lon Nol government by the Khmer Rouge became clearly imminent.
In December 1994, after a 26-year hiatus in diplomatic relations, the Philippines re-established its resident mission in Phnom Penh, and formally re-opened the Philippine Embassy in January 1995 with retired Lieutenant-General Thelmo Cunanan as Ambassador. 
From 1995, the following served as Ambassadors of the Philippines to Cambodia:

  • H.E. Thelmo Y. Cunanan          -           February 1995 to October 1998
  • H.E. Francisco E. Atayde         -           March 1999 to March 2001
  • H.E. Voltaire T. Gazmin            -           April 2002 to June 2004
  • H.E. Lourdes G. Morales          -           April 2006 to September 2008
  • H.E. Noe A. Wong                    -           September 2008 to September 2014
  • H.E. Christopher B. Montero    -           March 26, 2015 to May 22,  2019
The current Philippine Ambassador, H.E. Maria Amelita C. Aquino, assumed her post on 18 December 2020.
The Embassy manages the overall advancement of Philippine interests in the Kingdom of Cambodia and is assisted by a resident Office of Defense and Armed Forces Attaché. The Philippine Trade and Investment Center (PTIC) and the Special Agricultural Representative, both based in Bangkok, assist the Embassy in trade/commercial promotion and related activities.
The Embassy serves more than 7,000 Filipinos living and working in Cambodia, most of whom belong to the skilled labor sector.
The following are among the major agreements between the Philippines and Cambodia:
  • Agricultural and Agribusiness Cooperation (September 2015)
  • Cultural Agreement (June 2015)
  • Rice Trade (April 2013)
  • Air Services (April 2012 )
  • Recognition of Training and Certification for Seafarers (October 2002)
  • Health Workers' Development Cooperation (August 2000 )
  • Promotion and Protection of Investments (August 2000)
  • Establishment of a Joint Commission for Bilateral Cooperation (August 2000)
  • Visa Exemption for Diplomatic/Official Passport Holders (August 2000)
  • Tourism Cooperation (August 2000)
  • Rural Health Development Cooperation (December 1995)
  • Enhancement of Economic Trade Relations (December 1995)

Cooperation agreements in the areas of labor, sports, combatting transnational crimes, and tourism were signed during the State Visit to Cambodia of President Rodrigo R. Duterte on 13-14 December 2016.