Background Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. Researchers have tried to develop indices to assess liver fibrosis in NAFLD patients to avoid liver biopsy. In this study we aimed to compare fibrosis-4 (FIB-4), aspartate aminotransferase (AST) to platelet ratio index (APRI), and aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio with FibroScan for the assessment of hepatic fibrosis in patients with NAFLD. Methods This cross-sectional study included patients with NAFLD or non-alcoholic steatohepatitis (NASH) referred to the Gastroenterology Clinic of Shahid Mohammadi Hospital, Bandar Abbas, Iran, in 2019. Demographic features of the participants including age and gender were recorded. All participants underwent FibroScan and had their AST, ALT, and platelet count measured in a random blood sample, taken within 1 month of the FibroScan. Results Of the 205 NAFLD patients included in this study with a mean age of 42.95 ± 10.97 years, 144 (70.2%) were male. Fibroscan results revealed that 94 patients (45.9%) had F1, 67 (32.7%) F2, 29 (14.1%) F3, and 15 (7.3%) F4 liver fibrosis. A significant correlation was found between FibroScan score and FIB-4 (r = 0.572), APRI (r = 0.667), and AST/ALT (r = 0.251) (P < 0.001). Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of APRI at the 0.702 cut-off for the differentiation of F3 and F4 from F2 and F1 were 84.1, 88.2, 66.1, 95.3, and 87.3%, FIB-4 at the 1.19 cut-off 97.7, 72.7, 49.4, 99.2 and 78%, and AST/ALT at the 0.94 cut-off 61.4, 77, 42.2, 87.9, and 73.7% respectively. Moreover, the area under the receiver operating curve of APRI, FIB-4, and AST/ALT for the differentiation of F3 and F4 from F2 and F1 was 0.923, 0.913, and 0.720, respectively. Conclusions Based on these results, APRI appears to be the most appropriate substitute of FibroScan for the detection of significant fibrosis in NAFLD patients. FIB-4 was the second best, suggesting that in case of FibroScan unavailability, APRI and FIB-4 are the best indices to assess liver fibrosis in NAFLD patients.