Enterocytozoon hepatopenaei (EHP) is a microsporidian parasite that causes hepatopancreatic microsporidiosis (HPM) in penaeid shrimp. HPM was observed in several countries, including Thailand and India; it has become a prominent pathogen in shrimp culture. Based on observations on EHP infection in the wild, the route of transmission has been hypothesized. Identification of artificial EHP infection procedures can facilitate our understanding of EHP transmission. Experimental transmission of EHP was attempted using the immersion and oral infections of infection. In the immersion mode, post-larvae (PL) were exposed to an EHP tissue homogenate (0.2%) by immersion for 48 hr. Experimental samples were collected at various time points, and infection was confirmed using polymerase chain reaction, haematoxylin and eosin staining, transmission electron microscopy and modified trichrome staining. All test results revealed successful EHP transmission. Similar results were obtained through oral infection (oral infection). Innate immune gene expression patterns during infection were analysed; prophenoloxidase, crustin and superoxide dismutase were upregulated at 6, 6 and 48 hr post-challenge, respectively. Experimental infection procedures facilitate the development of diagnostic and prevention strategies. This is the first study demonstrating the experimental transmission of EHP in shrimp PL. © 2019 John Wiley & Sons Ltd