BackgroundCryptosporidiumis second only to rotavirus as a cause of moderate-to-severe diarrhea in young children. There are currently no fully effective drug treatments or vaccines for cryptosporidiosis. MicroRNAs (miRNAs) are involved in regulating the innate immune response toCryptosporidium parvuminfection. In this study, we investigated the role and mechanism of miR-3976 in regulating HCT-8 cell apoptosis induced byC. parvuminfection.MethodsExpression levels of miR-3976 andC. parvumburden were estimated using real-time quantitative polymerase chain reaction (RT-qPCR) and cell apoptosis was detected by flow cytometry. The interaction between miR-3976 and B-cell lymphoma 2-related protein A1 (BCL2A1) was studied by luciferase reporter assay, RT-qPCR, and western blotting.ResultsExpression levels of miR-3976 were decreased at 8 and 12 h post-infection (hpi) but increased at 24 and 48 hpi. Upregulation of miR-3976 promoted cell apoptosis and inhibited the parasite burden in HCT-8 cells afterC. parvuminfection. Luciferase reporter assay indicated thatBCL2A1was a target gene of miR-3976. Co-transfection with miR-3976 and aBCL2A1overexpression vector revealed that miR-3976 targetedBCL2A1and suppressed cell apoptosis and promoted the parasite burden in HCT-8 cells.ConclusionsThe present data indicated that miR-3976 regulated cell apoptosis and parasite burden in HCT-8 cells by targetingBCL2A1followingC. parvuminfection. Future study should determine the role of miR-3976 in hosts’ anti-C. parvumimmunity in vivo.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s13071-023-05826-w.