As of the census² of 2000, there were 41,082 people, 16,054 households, and 11,719 families residing in the county. The population density was 47 people per square mile (18/km²). There were 20,798 housing units at an average density of 24 per square mile (9/km²). The racial makeup of the county was 72.74% White, 23.58% Black or African American, 0.49% Native American, 0.18% Asian, 0.03% Pacific Islander, 2.03% from other races, and 0.94% from two or more races. 3.64% of the population were Hispanic or Latino of any race.

In 2005 74.0% of the population was non-Hispanic whites. 20.7% of the population was African-American. 4.6% of the population was Latino.

By 2006 Pender County had a population of 48,630, which represented an 18.4% increase in the population since 2000.

There were 16,054 households out of which 29.40% had children under the age of 18 living with them, 57.90% were married couples living together, 11.20% had a female householder with no husband present, and 27.00% were non-families. 22.90% of all households were made up of individuals and 8.50% had someone living alone who was 65 years of age or older. The average household size was 2.49 and the average family size was 2.90.

In the county the population was spread out with 23.20% under the age of 18, 7.40% from 18 to 24, 29.50% from 25 to 44, 25.80% from 45 to 64, and 14.10% who were 65 years of age or older. The median age was 39 years. For every 100 females there were 101.20 males. For every 100 females age 18 and over, there were 99.50 males.

The median income for a household in the county was $35,902, and the median income for a family was $41,633. Males had a median income of $31,424 versus $21,623 for females. The per capita income for the county was $17,882. About 9.50% of families and 13.60% of the population were below the poverty line, including 18.60% of those under age 18 and 14.40% of those age 65 or over.