As of the census of 2000, there were 861 people, 372 households, and 210 families residing in the borough. The population density was 6,184.9 people per square mile (2,374.5/km²). There were 395 housing units at an average density of 2,837.4/sq mi (1,089.4/km²). The racial makeup of the borough was 93.96% White, 0.23% Native American, 0.23% Asian, 3.72% Pacific Islander, 1.39% from other races, and 0.46% from two or more races. Hispanic or Latino of any race were 8.71% of the population.
There were 372 households out of which 28.0% had children under the age of 18 living with them, 40.3% were married couples living together, 12.9% had a female householder with no husband present, and 43.5% were non-families. 38.7% of all households were made up of individuals and 18.8% had someone living alone who was 65 years of age or older. The average household size was 2.24 and the average family size was 2.97.
In the borough the population was spread out with 25.2% under the age of 18, 8.5% from 18 to 24, 30.3% from 25 to 44, 20.9% from 45 to 64, and 15.1% who were 65 years of age or older. The median age was 36 years. For every 100 females there were 96.6 males. For every 100 females age 18 and over, there were 92.8 males.
The median income for a household in the borough was $28,125, and the median income for a family was $33,594. Males had a median income of $26,563 versus $20,125 for females. The per capita income for the borough was $14,394. About 10.7% of families and 13.7% of the population were below the poverty line, including 18.1% of those under age 18 and 17.0% of those age 65 or over.
There is a large amount of Amish and Mennonite population around the borough.
Pennsylvania Route 35, a southwest-northeast highway that serves as Juniata County's principle arterial highway running in that direction, forms the main street of Mifflintown. It intersects the former mainline of US routes 22 and 322, which was moved in the early 1970s to a four-lane bypass lying east of the town. The former Pennsylvania Railroad mainline tracks, now owned by the Norfolk Southern Railway, lie across the Juniata River in the adjoining town of Mifflin.