The need to use complex in vitro cell culture, expensive equipment and highly-trained technicians that are available only to specialist laboratories has significantly limited studies assessing the potential of pulsed UV light (PUV) to inactivate the waterborne parasite Cryptosporidium parvum in drinking water. This constitutes the first study to report on the use of different non-pathogenic Bacillus endospores as potential surrogate organisms to indicate the PUV inactivation performance of C. parvum oocyst suspended in water. Findings showed that PUV effectively inactivated ca. 5 log10 CFU/ml B. megaterium and B. pumilus endospores suspended in water at a UV dose of 9.72 μJ/cm2 that also inactivated statistically similar levels of C. parvum oocysts (P <0.05) as determined by combined in vitro HCT-8 cell culture and qPCR. Specifically, this study demonstrated that Bacillus megaterium exhibited greater or similar PUV inactivation kinetic data compared to that of similarly treated C. parvum over the UV dose range 6.4 to 12.9 μJ/cm2. Therefore, the former may be used as indicator organism for safely investigating the PUV-inactivation performance of this chlorine resistant waterborne parasite at waste water treatment plant level. Findings presented will impact positively on future water quality studies and on public health.