The pleiotropic effects of high-density lipoprotein (HDL), including its protective properties against sepsis, are attributed to the sphingosine 1-phosphate and apolipoprotein M (ApoM) that are carried on the lipoproteins. In this study, we attempted to elucidate the possible mechanisms underlying the sepsis coagulopathic state by considering the modulation of NETosis. Our results revealed that in a lipopolysaccharide-induced sepsis mouse model, the levels of NETosis markers, such as plasma DNA and histone, were elevated in ApoM-knockout (KO) mice and attenuated in ApoM-overexpressing mice. In ApoM-KO mice, the survival rate decreased and the occurrence rates of coagulopathy and organ injury increased following the administration of histone. Treatment with a conditioned medium of ApoM-overexpressing cells attenuated the observed NETosis in HL-60S cells that differentiated into neutrophils and were inhibited through the suppression of S1P1 or S1P4. The attenuation of PKCδ and PKCα/β by S1P1 and S1P4 activation may also be involved. In ApoM-overexpressing mice, coagulopathy and organ injuries were attenuated following an injection of histone; these effects were partially inhibited by S1P1, 3, S1P4, or S1P1 antagonists. Furthermore, the exogenous administration of ApoM protected ApoM-KO mice that were challenged with histone from developing NETosis. In conclusion, the ApoM/S1P axis protects against NETosis through the attenuation of PKC activation by S1P1 and S1P4. The development of drugs targeting the ApoM/S1P axis may be beneficial for the treatment of pathological conditions involving uncontrolled NETosis, such as sepsis.