Brookhaven is located at 39°52'9" North, 75°22'56" West (39.869167, -75.382500).
According to the United States Census Bureau, the borough has a total area of 1.70 mi2 (4.41 km2). 1.70 mi2 (4.40 km2) of it is land and 0.01 mi2 (0.01 km2) of it is covered by water. The total area is 0.32% water.
Brookhaven is located in the Eastern Standard Time (EST) timezone, GMT-05:00. It observes Daylight Saving Time (DST).