The community was organized in 1909, in part, due to the efforts of John Closner.
The city is known for the Basilica of Our Lady of San Juan, one of the largest churches in the Rio Grande Valley.
San Juan is located in southern Hidalgo County at  in the Rio Grande Valley region. It is bordered to the west by the city of Pharr and to the east by the city of Alamo. Unincorporated communities bordering San Juan include Lopezville to the northwest, Murillo to the north, and North Alamo to the northeast. San Juan is 5 miles (8 km) east of McAllen and 8 miles (13 km) south of Edinburg, the county seat. It is 10 miles (16 km) north of the Mexican border at the Pharr–Reynosa International Bridge over the Rio Grande.(26.192451, -98.152708),
As of the census of 2000, there were 26,229 people, 6,606 households, and 5,952 families residing in the city. The population density was 2,383.0 people per square mile (919.8/km²). There were 7,719 housing units at an average density of 701.3 per square mile (270.7/km²). The racial makeup of the city was 4.4% White, 0.34% African American, 0.8% Native American, 0.09% Asian, 0.03% Pacific Islander, 15.93% from other races, and 1.89% from two or more races. Hispanic or Latino of any race were 95.12% of the population.
There were 6,606 households out of which 56.7% had children under the age of 18 living with them, 69.0% were married couples living together, 17.1% had a female householder with no husband present, and 9.9% were non-families. 8.6% of all households were made up of individuals and 4.2% had someone living alone who was 65 years of age or older. The average household size was 3.95 and the average family size was 4.19.