Pancytopenia manifests as a reduction in circulating myeloid, erythroid, and megakaryocytic cell lines, with causes ranging from infectious, neoplastic, and immune-mediated diseases to sepsis and various drugs. This study endeavors to pinpoint the etiological agents of pancytopenia and establish parameters for distinguishing sepsis from non-sepsis cases. Clinical signs indicative of bleeding tendency and sepsis were identified, and animals exhibiting pancytopenia upon hematological analysis underwent further evaluation, including hemato-biochemical analysis, bone marrow cytology, PCR analysis, and flow cytometry, to ascertain the underlying causes. Discriminant function analysis was performed on 12 parameters obtained from 37 pancytopenic dogs and 20 healthy dogs, with the objective of distinguishing between sepsis and non-sepsis cases. Mean fluorescence intensity levels against platelets were recorded at 24.6% and against RBCs at 26.1%, confirming the presence of immune-mediated thrombocytopenia and anemia. Over a span of 2 years, the incidence of pancytopenia was higher in young animals. In our study, the identified etiologies among pancytopenic dogs were predominantly hemoprotozoan infections, accounting for 62% (41 dogs), followed by immune-mediated diseases at 24% (16 dogs). Significantly, five parameters - erythrocyte count, leukocyte count, platelet count, temperature, and heart rate were identified as significantly discriminatory between dogs with sepsis and those without sepsis. The higher incidence of pancytopenia in young animals can be attributed to infectious and secondary immune-mediated diseases. Among the different hemato-biochemical, physical parameters leukocyte count followed by RBC count was found to be the suitable parameters to differentiate sepsis and cases without sepsis in pancytopenic cases. This was also confirmed by the area under the curve of more than 80% and 78%, respectively, in the receiver operating curve, and 100% of originally grouped cases were correctly classified at a 99% confidence interval.