A batch processing control system for a shell egg pasteurizer controls the time and temperature in which batches of shell eggs are held in a pasteurization bath in accordance with a predetermined pasteurization protocol for designated egg size and start temperature. The predetermined pasteurization protocol is preferably statistically verified to optimize batches of eggs having the designated size and start temperature. The system also includes reporting software that generates daily reports to track each respective batch and verify that the batch has been pasteurized according to the statistically verified protocol.
