A simple ion chromatographic (IC) method was developed and validated for simultaneous or individual determination of zoledronic, alendronic, pamidronic acids and their related substances in pharmaceutical formulation. The analytes were separated on Waters IC-Pak Anion HR analytical column with a nitric acid (3 mM) without any other additives, as mobile phase at a flow rate of 1.0 mL min−1. Inverse UV detection was used at 240 nm. Important chromatographic factors that influence the chromatography responses were screened by 11/12 Pluckett–Burman design and their interaction were assayed by 23 full factorial design. The RP-HPLC method was optimized with the aid of LC-Simulator® (ACD Labs, Toronto, Ontario, Canada) software. Validated method was successfully used for quantitative analysis of PAMIFOS®, concentrate for infusion (Habitfarm AD, Ivanjica, Serbia), ZOMETA®, powder for infusion (Novartis Pharma, Stein AG, Switzerland) and BONAP® tablets (Hemofarm, Vrsac, Serbia). Total chromatographic analysis time per sample was approximately 6 min, which represents significant improvement over existing methods. Validation studies revealed that the method is specific, rapid, reliable, and reproducible. Calibration plots were linear over the concentration ranges 20–120 μg mL−1 and 0.1–2 μg mL−1 for bisphosponates and their related substances, respectively. The LODs were 8.7, 4.7, 2.5, 0.026 and 0.011 μg mL−1 for alendronate, pamidronate, zoledronate, phosphoric acid and phosphorous acid, respectively.