After his graduation in the PMA, Nafarrete was commissioned as a
second lieutenant and was later named as a platoon commander of Alpha Company of the 10th Infantry Battalion, which is under the 1st Infantry Division. He later became a pioneer in organizing the 1st Scout Ranger Company of the
1st Scout Ranger Regiment during its reactivation in 1991. Nafarrete later served under various infantry and special forces units, primarily under the 1st Scout Ranger Regiment, and was deployed to counter
New People’s Army (NPA) units across
Kalinga,
Apayao, the
Negros Island,
Cotabato, and
Maguindanao; as well as
Abu Sayyaf terrorists in the
Zamboanga Peninsula and
Basilan. In 1996, Nafarrete served as the commander of the 6th Scout Ranger Company, a Scout Ranger unit serving under the
6th Infantry Division. In 1997 to 1999, Nafarrete would later serve as intelligence and operations officer of the 2nd Scout Ranger Battalion, and later as an intelligence officer of the
1st Scout Ranger Regiment. During his years as a senior officer, Nafarrete served under the
AFP Joint Special Operations Group, and later became the battalion commander of the 1st Scout Ranger Battalion from 2008 to 2010. After his stint as battalion commander of the 1st Scout Ranger Battalion, Naffarete was later placed under the
Presidential Security Group (PSG) from 2011 to 2015, where he serves as the group's Assistant Chief of Staff for Operations, G3, Stage Commander, Head of Security, and as Chief of Staff. Naffarete also monitored security operations of former President
Benigno Aquino III, as well as visiting foreign heads of state and dignitaries, and later served as the Chairman of the Government of the Philippines’ Coordinating Committee on the Cessation of Hostilities. During his stint as the division commander of the 1st Infantry Division, Nafarrete led intensified military operations against the NPA, which is tasked to dismantle the NPA's final guerilla front in the region, known as the Western Mindanao Regional Party Committee, while continuing development initiatives in conflict-affected communities. On 23 July 2024, Nafarrete was named as the division commander of the
6th Infantry Division, where he later oversaw counter-terrorism operations against the NPA and the Dawlah Islamiya. Nafarrete also led civil-military operations that led to the surrender of a variety of NPA members, as well as 420
Bangsamoro Islamic Freedom Fighters and Dawlah Islamiya members. On 20 November 2024, Nafarrete was named as the Acting Commander of the AFP
Western Mindanao Command (WESTMINCOM), where he replaced Lieutenant General William N. Gonzales and later served as the command's commander. As the commander of WESTMINCOM, Nafarrete spearheaded intensified multi-domain operations against the remnants of the NPA, Abu Sayyaf, and Dawlah Islamiya, and also intensified community peacebuilding initiatives in the
BARMM. Nafarrete also oversaw election seccurity measures amidst the
2025 Philippine general election.
Commanding General of the Philippine Army On 31 July 2025, Nafarrete was named as the new
Commanding General of the Philippine Army (CGPA) and replaced Lieutenant General
Roy Galido, who is retiring after ending his two-year fixed term. During his assumption speech, Nafarrete highlights his command's focus on human capital development, and emphasized the importance of every soldier. Nafarrete's five-point command guidance tackles on personnel, morale, physical & mental well-being, education, and finances, while also continuing the army's modernization programs through the procurement of new systems and modern hardware to enhance the army's overall capabilities. During his term as the CGPA, Nafarrete initiated plans to integrate drones in the army's external defense operations and expand the usage of
drone warfare in the army's defense doctrine to all units ranging from both active and reserve units, and highlighted the usage of drones in the modern battlefield, citing the successful usage of drones for various military operations on the
Russian invasion of Ukraine. Nafarrete also expanded the integration and training of the army reserve units with regular army units to sustain the army's capabilities and professional development. Nafarrete also laid out proposals to upgrade the present Army Artillery Regiment (AAR) to the Army Artillery Command (AAC), which will allow the Army to increase its abilities aside from the current short to long-ranged howitzers and mortar systems currently in service, and laid out procurement plans for medium-ranged weapons systems and ground-based air defense systems, which includes both gun-based and missile-based systems. The plan could also allow the AFP Strategic Command to lay out plans for procuring long-ranged weapons systems. ==Awards from military service==