A high performance capillary electrophoresis (HPCE) method with UV detection at 214 nm was developed for the assay of FR 900098 (a promising better antimalarial drug in the class of fosmidomycin). Optimization of the analytical parameters resulted in an organic modifier (methanol) concentration of 15%, 0.2 mM hexadecyl trimethyl ammonium bromide (HTAB) and phosphate buffer (14 mM KH₂PO₄/56 mM K₂HPO₄) with adjusted PH to 10.9 by 1M sodium hydroxide. Under these conditions the migration time of FR 900098 was 7.6 minutes in human serum. Validation of the analytical method showed good recoveries, precision and accuracy. The limit of detection (LOD) and limit of quantification (LOQ) in human serum was 0.5 µg/ml and 1.0 µg/ml respectively. FR 900098 solutions were stable for short time (a day), freeze-thaw and long term (six months). This technique will be useful as a fast and accurate analytical method for FR 900098 pharmaceutical dosage assays and pharmacokinetic studies.