Background: Inflammatory markers are regarded as prognostic factors of the outcomes of hepatocellular carcinoma (HCC). Examples include the neutrophil-to-lymphocyte ratio (NLR); platelet to lymphocyte ratio (PLR); the albumin and lymphocyte counts used in the prognostic nutritional index (PNI); and the neutrophil, lymphocyte, and platelet counts used in the systemic immune-inflammation index (SII). This study evaluates the effects of PNI, NLR, PLR, and SII to predict recurrence and survival in patients with Barcelona Clinic Liver Cancer (BCLC) stages 0-A of HCC after hepatectomy. Methods: This retrospective study was conducted at Kaohsiung Chung-Gung Memorial Hospital, Taiwan. The study enrolled 891 patients (77.9% males; mean age 58.53 ± 11.60 years) with BCLC stage 0/A HCC undergoing hepatectomy between 2001 and 2016. PNI, NLR, PLR and SII were measured before hepatectomy. Results: High NLR (>1.8) was adversely associated with overall survival (p = 0.032). Low PNI (≤45) was adversely associated with overall survival and disease-free survival (p < 0.001). Low SII (≤45) also had an adverse association with overall survival (p = 0.008) and disease-free survival (p < 0.001). Diabetes mellitus, cirrhosis, microvascular invasion, low PNI (≤45), and low SII (≤160) were independently associated with poor overall survival in a multivariate analysis. HCV infection, diabetes mellitus, cirrhosis, microvascular invasion, low PNI, and low SII were independent prognostic factors of recurrent HCC. The combined use of PNI and SII provided improved prognostic information. Conclusions: Low PNI and low SII are significantly poor prognostic factors for overall survival and recurrence in patients with BCLC 0-A hepatocellular carcinoma after hepatectomy.