[6] European-American settlers founded the village in April 1885, naming it in honor of the Scottish politician and businessman Sir John Pender, a pioneer of the Transatlantic Cable.

He founded what is now Cable & Wireless Worldwide, and was a director of the Chicago, St. Paul, Minneapolis & Omaha Railway.

[7] Tribal authorities of the federally recognized Omaha Nation assert that Pender is within the boundaries of the reservation as defined in its 1865 treaty with the United States.

However, a Nebraska state court held in 1999 that the western boundary was a railroad right-of-way east of Pender, because of Omaha land sales to white farmers over the decades.

The tribe's response is that the state does not have the power to redefine the boundary set by the Omaha treaty with the US government in 1865.

[8] The boundary and jurisdiction issues have received recent testing related to traffic control and liquor sales.

[9] Seeking to gain revenue from "nuisance" businesses, the Omaha in 2006 passed a law establishing the requirement for liquor merchants to pay the tribe license fees and a 10% sales tax to operate within the reservation.

While the case was pending, the judge ordered a temporary stay on the merchants' paying the liquor sales tax to the Omaha Tribe.

The plaintiffs had submitted a detailed report to them by an expert witness on transactions related to Pender and the western boundary.

[12] On March 22, 2016, the Supreme Court unanimously held that Pender was within the boundaries of the Omaha Indian reservation.

According to the United States Census Bureau, the village has a total area of 0.71 square miles (1.84 km2), all land.