Introduction: Endotoxin removal is a crucial stage in ensuring the safety of parenteral products. S3E3-S-Sepharose, which has been generated via site-specific immobilization of the S3E3 cationic amphiphilic peptide (CAP) on Sepharose, is a newly designed affinity matrix proposed for lipopolysaccharide (LPS) removal from biopharmaceuticals and vaccines. Methods: In the current study, the kinetic behavior of LPS adsorption on the matrix was investigated at pHs 4.5 and 8.5 by incubation of LPS-contaminated bovine serum albumin (BSA) solutions, as a model, with the S3E3-Sepharose matrix at different incubation times in a batch-wise mode. Various mathematic models were employed to explain the amount of adsorbed LPS, and the normalized root mean square error (NRMSE), relative prediction error (RE), and relative percentage error (RPE) were utilized to identify the best-fitting model. Results: The kinetics study revealed that the pseudo-second-order (PSO) reaction, and pore diffusion mass transfer were the rate-controlling steps of LPS adsorption on the S3E3-S-Sepharose and pH of samples did not affect the LPS adsorption kinetics. Conclusion: These findings provide valuable insights for scaling up the LPS removal process through affinity chromatography, contributing to advances in biopharmaceutical and vaccine production research.