This study was performed to assess the ability of Clostridium perfringens types A and D to induce immunological and inflammatory alterations, and mortalities in Nile tilapia (Oreochromis niloticus). Healthy Nile tilapia (n = 90) with an average body weight of 35 ± 0.5 g were randomly divided into three triplicate groups with ten fish in each aquarium. Fish were injected intraperitoneally (IP) with 0.1 mL of 2.4 × 108 CFU/mL of C. perfringens type A in the first group (G1) and type D in the second group (G2). Fish in the third group (G3) were IP injected with sterile saline and served as control. Clinical signs and postmortem lesions of infected fish started appearing on day 1 post-infection (PI), and the cumulative mortality rates were recorded as 50%, 73%, and 0% in G1, G2, and G3 groups, respectively. Superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) activities in the G1 and G2 showed a significant gradual decrease, and reached a peak on day 14, compared to the control group, whereas malondialdehyde (MDA) activity was significantly increased at all-time intervals in G1 and G2. TNF-α showed a significant increase only on day 14 in G1 and G2 compared to the control group. Myeloperoxidase activity (MPO) of both G1 and G2 was increased significantly on day 7 and day 14 compared to the control group and other time periods of exposure. Nitric oxide (NO) activity decreased gradually at 24 h and on day 7 and day 14 for G1 and G2, respectively. The inflammatory biomarker IL-1β showed a significant gradual increase, which reached a peak on day 7 for both G1 and G2 in comparison to control. IL-6 reached a peak on day 14 for G1 and on day 7 for G2. Significant down-regulation of IL-10 occurred on days 7 and 14 post challenge. There was a gradual increase in serum proteins in G1 and G2, which attained a peak on day 14, except γ-globulin, which showed a significant decrease in the same trend. The albumin level decreased gradually in G1 and G2, and among the different periods, and reached a peak at 24 h, followed by on day 7 and finally, on day 14. Lysozyme activity and IgM initially showed a significant increase at 24 h in the G1 and G2 groups compared to the control group and other time periods of exposure; later, decreased gradually on day 7 and day 14. There was a significant decline in complement 3 in G1 and G2 on day 14, followed by day 7 and a significant increase at 24 h. This study has shown that C. perfringens types A and D could be important causative agents of disease and mortality in cultured Nile tilapia species.