In this work, rhamnolipid biosurfactant as an eco-friendly and biodegradable cleaning agent was produced by Pseudomonas aeruginosa bacteria and was used to evaluate the chemical cleaning efficiency of whey fouled ultrafiltration membranes. Thin layer chromatography (TLC) and Fourier transform infrared spectroscopy (FTIR) confirmed the successful synthesis of rhamnolipid. The produced rhamnolipid was compared to chemical cleaners including sodium hydroxide (NaOH), sodium dodecyl sulfate (SDS) and Tween 20. Ultrafiltration membranes used for fouling and cleaning analysis were prepared using phase inversion via immersion precipitation technique. For studying the fouling mechanisms, Hermia's model adapted to cross-flow was used. From the fouling mechanism experiments, it was found that the complete blocking and cake formation were the dominant fouling mechanisms. The highest values of cleaning efficiency were achieved using rhamnolipid and NaOH as cleaning agents with the flux recovery of 100%, but with considering the low concentration of the rhamnolipid used in the cleaning solution compared to NaOH (0.3 versus 4 g/L for NaOH), its application is preferred.