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<i>Aeromonas schubertii</i> is the etiological pathogen of internal organ nodules in snakehead fish. Infections with <i>A. schubertii</i> produce a significant economic loss in aquaculture. Therefore, it is important to examine the immune mechanisms by which snakeheads defend against <i>A. schubertii</i> infection. In this study, we established a hybrid snakehead infection model by intraperitoneal injection of <i>A. schubertii</i> that produced internal organ nodules. The splenic immune response of infected fish was examined at the transcriptome level by Illumina-seq analysis. Results showed 14,796 differentially expressed genes (DEGs) following <i>A. schubertii</i> infection, including 4441 up-regulated unigenes and 10,355 down-regulated unigenes. KEGG analysis showed 2084 DEGs to be involved in 192 pathways, 14 of which were immune-related. Twelve DEGs were used to validate quantitative real-time PCR results with RNA-seq data. Time-course expression analysis of six genes demonstrated modulation of the snakehead immune response by <i>A. schubertii.</i> Furthermore, transcriptome analysis identified a substantial number of DEGs that were involved in the apoptosis signaling pathway. TUNEL analysis of infected spleens confirmed the presence of apoptotic cells. This study provided new information for a further understanding of the pathogenesis of <i>A. schubertii</i> in snakeheads, which can be used to prevent and possibly treat <i>A. schubertii</i> infections.