We live-trapped black-tailed prairie dogs on Buffalo Gap National Grassland, South Dakota, 2020-2021. We anesthetized trapped animals (and their fleas) with isoflurane in induction chambers for processing. We combed each individual with a fine-tooth comb for 30 seconds to remove and count fleas. The total flea count from an individual prairie dog was considered an index of flea abundance. We released all animals, after they were recovered from anesthesia, at the location where they were captured. Data were collected on sites treated with fipronil "FipBit" bait pellets for systemic flea control with prairie dogs. Sites were treated with FipBits containing 0.68, 0.71, or 0.83 milligrams of fipronil per FipBit. The FipBits were applied along transects at a rate of 125/hectare. Data were collected 12 July–2 September 2020 (assessing flea abundance before treatments), 9-23 September 2020 (evaluating flea control over ~1 month) and June–July 2021 (evaluating flea control over 9-10 months). The data set (South Dakota FipBits Fleas 2020-2021.csv) includes data from captures of individual prairie dogs and lists treatment (TREATMENT = 0.68, 0.71, or 0.83 milligrams of fipronil per FipBit), flea abundance (FLEAS), and period of experiment (PERIOD = BEFORE [before treatments], AFTER1 [~1 month post-treatment], and AFTER910 [~9-10 months post-treatment). Funding and logistical support were provided by the US Geological Survey; Prairie Wildlife Research; National Park Service; US Forest Service; and US Fish and Wildlife Service.