The town was named in his honor by Augustinian friars during the Spanish colonization in 1586, following the tradition of dedicating settlements to Christian saints.

Saint John the Baptist's significant role in biblical history particularly his call for repentance and his baptism of Jesus in the Jordan River made him an ideal patron for the municipality.

In the early history, San Juan was originally a settlement of the Ilocano group called Samtoy and was known as Dalandan, named after the native fruit (Citrus × aurantium L.) that grew abundantly in the area.

The people in this settlement practiced animistic religion and were actively engaged in trading goods with neighboring areas, including the Igorots from the highlands, Pangasinans, Tagalogs, and even traders from Maritime Southeast Asian countries, China, and Japan.

According to historian William Henry Scott, goods such as gold, beeswax, ceramics, porcelain, beads, and metals were exchanged in this trade network.

[6] In 1582, the area of San Juan was proclaimed a mission station under the authority of the Augustinian Order and was initially named Baratao, as recorded in the Nueva Segovia Bi-centennial souvenir booklet dated April 25, 1587.

On March 2, 1850, San Juan became part of the province of La Union, which was created by Governor-General Antonio Maria Blanco.

Another local resident, also named Mariano Gaerlan, wrote Biag ti Maysa a Lakay, Wenno Nakaam-ames a Bales (i.e., Life of an Old Man, or a Dreadful Revenge) under the pen-name of Batallador.

On January 19, 1942, Gaerlan co-led the first guerrilla ambush against Japanese forces in the Philippines, which was prosecuted on the southern outskirts of Candon.

He was subsequently appointed commander of the Third Battalion of the 121st Infantry Regiment of the United States Armed Forces in the Philippines – Northern Luzon (USAFIP-NL).

Gaerlan was killed and subsequently beheaded later that same year at San Juan after he was betrayed by the local chief of police while visiting his sister.

San Juan was liberated in 1945 by the soldiers of the 121st Infantry Regiment, Philippine Commonwealth Army, USAFIP-NL and guerrillas of the La Union Infantry Regiment during the Battle of San Fernando under Major Russell W. Volckmann on their way to meet the liberating forces of General Douglas MacArthur on the beaches of Lingayen Gulf.

Subsequent government-sponsored irrigation systems and farm technicians led to a slow but assured recovery with increased productivity and profitability.

San Juan is located in the west of the province of La Union, along the Manila North Road, between latitudes 16°39'N and 16°43'N and longitudes 120°9'E and 120°15'E.

The topography of the town is characterized by hilly and mountainous terrain that gradually rises eastward from its coastal plains along the foothills of the Cordillera Central.

These barrios were Ili, Barraca, Panicsican, Talogtog, Sabangan, Taboc, Lubing, Sinapangan, Cacapian, Caculangan, Santa Rosa, Caaniyan, Oaquing, Catdongan, Caarusipan, Guinguinabang, Bugbugcao, Pacpacac, Legleg, Nadsaag, Capacuan, Bacnotan, Dasay, Al-langigan, Bombuneg, Balballosa, Duplas and San Felipe.

[7] As of the census of 2000, San Juan was home to 30,393 indigenous Ilocano people, concentrated in six barangays along the national highway.

San Juan is home to several thriving cottage industries, including damili (pottery), which produces items such as pots, animal feed containers, well pipes, decorative pottery, roof tiles, and traditional Ilocano earthenware such as burnay (earthen jars) and dalikan (firewood stoves).