Fernando Air Base was built over what used to be a sugarcane plantation by the United States Army before the outbreak of the Pacific War in 1941.

In the early 1942, it was occupied by the 16th Division of the Japanese Imperial Army under a General Morioka. The airfield was repaired and expanded and was called as Lipa West Airfield as reflected on a sketch in the diary of Colonel Tonegi, Commanding Officer of the 33rd Air Sector, 149th Airfield Battalion.

The airfield was used as one of the staging points of the kamikaze missions in the later part of 1944 during the outbreak of the Second World War.

American bombers rendered the airfield unusable for the Japanese with an incredibly precise bombing run right down the center of the runway on 14 February 1945.

In 01 May, the 11th Airborne Division of the United States Army captured Mount Malipunyo and the 127th Airborne Engineer Battalion proceeded to build a new base around the Lipa Airfield, lengthening the runway to accommodate C-47 transport aircraft. Upon completion, the combat troops conducted refresher classes.

This base was used as the staging point for the parachute drop at the Calamaniugan Airfield near Aparri Cagayan. On 22 June 1945, 54 C-47 Skytrains,13 C-46 Commandos, six Waco CG-4A and one CG-13 glider of the 317th Troop Carrier Group under Colonel John Lackey were prepositioned at the Lipa Airfield for the mission. On 23 June, the 1,030 officers and men of the Gypsy Task Force consisting of paratroopers from the 1st Battalion, 511th Parachute Infantry Regiment reinforced with Companies G and I from the 3rd Battalion; Battery C of the 457th Parachute Field Artillery Battalion; detachments of the 511th Airborne Signal Company; 711th Airborne Ordnance Company, and 511th PIR Service Company; the 2nd Platoon of the 221st Medical Company; the 11th Parachute Maintenance Company; the 1st Platoon of Company C, 127th Airborne Engineer Battalion; the demolition platoon of headquarters and HQ Company, 511th PIR; and language and chemical detachments from the 11th Airborne Division headquarters, were transported by Col Lackey and his troops to Calamaniugan with the goal of joining the last battle of Cagayan Valley. This was part of the strategy to cut the escape routes of the remaining Japanese forces in Luzon.

After the war, the Philippine Army Air Corps was reactivated. Its first flying unit, the First Troop Carrier Squadron was activated on 01 September 1945 at the Lipa Airfield under Captain Roberto H Lim as the first Commander. He started with only two C-47 Skytrains but he was able to build up a fleet of 22 Gooney Birds until he left in January 1946.

Captain Lim was born on 05 February 1920 to General Vicente Lim and Pilar Hidalgo Lim. He entered the Philippine Military Academy as a plebe on 01 April 1937 and was sent to the US Naval Academy in Annapolis, Maryland where he graduated in 1941.

In 1946, Lipa Airfield was renamed as Lipa Army Air Base and subsequently, to Lipa Air Base on 21 January 1948.

In 12 April, President Manuel Roxas directed the renaming of the Lipa Air Base to Fernando Air Base in honor of Lieutenant Colonel Basilio Fernando who was the first sworn PAAC Commander when it got drafted into the USAFFE on 15 August 1941 with 141 pilots, 17 ground officers, 1,200 enlisted men and 64 planes. He was born on 14 June 1895 in San Mateo, Rizal.

On 22 September 1952, Fernando Air Base became a training base with the activation of the 100th Training Wing pursuant to General Order # 38 Headquarters Philippine Air Force with Major Pedro Q Molina PAF as the first Commander.

The Philippine Air Force Flying School was formed when the 101st and 102nd Pilot Student Squadrons were established in Fernando. The T-34 Mentor and T-28 Trojan were used for primary and basic flying training. The PT-13 Stearman and T-6 Texan were also flown by earlier classes.

The Philippine Air Force Technical School was established on 10 March 1950.

The 511th Dental Dispensary which was established on 19 December 1950 and 504th Medical Air Evacuation Flight attached to the Troop Carrier Squadron on 25 February 1946 were housed in one building in 1950s. These units evolved to be the Fernando Air Base Hospital and 1303rd Dental Dispensary.

The Air Force Officer School became part of the Wing on 01 July 1953 which necessitated its transfer from Nichols to Fernando.

The 550th Air Base Group was activated on 02 August 1960 and the 440th Maintenance and Supply Group was activated on 01 September 1960.

In 1961, AFOS became the Air Command and Staff College and relocated to Nichols until it was reactivated on 09 May 1969.

In 1968, the T-41D Mescalero fleet was added to the inventory replacing the T-34. Class 70A was the first to use these aircraft.

The Non-Commissioned Officer Academy was established on 17 January 1972 per General Order #273 HPAF. The first NCO course was started on 05 June 1972.

In 1973, the Wing acquired SF-260 Marchetti trainers which eventually replaced the T-28.

On 11 November 1974, the 104th Composite Tactical Squadron of the PAFFS was organized to take charge of the mobile training conducted in the different bases using all types of aircraft except fighter planes.

Around 1985, the surviving SF-260 Warriors from the 17th Attack Squadron of the 15th Strike Wing were transferred to the Flying School as additional trainer planes.

In 1988, the 440th Maintenance and Supply Group was deactivated and all its personnel and squadrons were placed under the Flying School.

In 1990, the Wing acquired S211 jet trainers which were first used by Class 91.

Lieutenant Gernale and Lieutenant Ignacio were the first female graduates of the Undergraduate Pilot Training in 1993. Lt Junio of Class 1992 was the first female student under the said training. Unfortunately, she died in an accident during the specialization training on the MD-520 MG.

In 1992, the 440th Maintenance and Supply Group was reactivated.

In July 1993, 18 SF-260 Turbo Prop trainers were acquired to replace the SF-260 Marchetti. In 2001, these trainers were transferred to the 17th Attack Squadron of the 15th Strike Wing.

The first batch of female aviation cadets entered in 1993 and graduated as members of Class 1995 – Lieutenant Bergardo, Lieutenant Catunao, Lieutenant Kalalo, Lieutenant Salon, and Lieutenant Salvosa.
In 1997, the Task Force Valentine was formulated because of the severe backlog of training operations due to unfavorable weather conditions. All T-41D trainers were moved to Rajah Buayan Air Station in General Santos City and the training camp was inaugurated as Philippine Air Force Training Center.

On 16 June 1998, the Philippine Air Force Aviation Officer Candidate School was established. The first class trained under the 12-month program was 99A.

In 1999, the 440th Maintenance and Support Group was deactivated and placed under PAFFS.

On 21 September 1999, the Air Education and Training Command was activated pursuant to General Order # 299 HPAF with Brigadier General Benjamin P Defensor Jr as the first commander.

On the same day, the NCO Academy was renamed as NCO School.

On 16 June 2000, the Basic Military Training School was established with the pioneer Basic Military Training Class of 2000.

In the middle of training of the PAFAOCS Class 2001A, the School was renamed as PAF Officer Candidate School in line with the deactivation of the AFP Officer Candidate School in Tanay, Rizal in 1997 and its subsequent decentralization to the major branches of service.

On 16 January 2002, the Air Power Institute was activated pursuant to General Order # 03 Headquarters Philippine Air Force.

In 2003, the Command acquired four SF-260 Marchetti planes on a rent-to-own basis.

In 2004, after the deactivation of the AFP Joint Command and Staff College, the Air Force Officer School was reactivated.

In 2005, the 440th Aircraft Maintenance Group was reactivated and the Air Power Institute was placed under the supervision of the OA-5.

The Command was adjudged as Model Base and CG, PAF Streamer awardee for the first time in 2007.

On 06 January 2009, the first NCO Alumni Homecoming dubbed as “Balik Yakap NCOS” was held with 800 attendees.

On 04 March, the Command acquired 15 T-41B aircraft donated by South Korea.

In June, the first class under the 15-month PAF Regular Officer Procurement Program graduated from PAFOCS. Also, the conduct of the Probationary Officer Training Course was transferred to the School from the Air Reserve Command.

In the same year, the Command was adjudged as the PAF Model Base and CG, PAF Streamer Awardee. Also, the winning AETC Hymn composed by SSg Wilson Balidio was adopted.

In 2010, the NCO School conducted Basic NCO Course in Mactan, Basa, Clark and Zamboanga through Mobile Training Teams in order to hasten the basic training of junior enlisted personnel.

From 04 November 2010 to June 2011, the Command acquired 18 SF-260 FH aircraft.

The Command was awarded as the CG, PAF Streamer for three consecutive years from 2010 to 2012 and Model Base from 2011 to 2013.

In 2011, the T-41 aircraft fleet was brought to Clark Air Base, Pampanga during the primary training phase of MPT Class 2012 due to unfavorable weather conditions in Fernando.

Major renovations, acquisition of equipment, and constructions took place within the base.

On 07 January 2014, the AFOS was transferred from Villamor to Fernando.

On 01 April 2016, Major General Galileo Gerard R Kintanar Jr Armed Forces of the Philippines assumed command of the AETC.

On 05 July, Fernando Air Base was adjudged as the PAF Model Base and Best Marching Unit. The Command also won in PAF-wide Feature Writing and Photo Essay contests.

Finally, pursuant to General Order Nr 299 HPAF, AETC was renamed as the Air Education, Training and Doctrine Command effective 23 August 2016 with the Air Power Institute back under its control.