Endophytic fungi are a rich source of novel organic compounds with interesting biological activities and a high level of biodiversity. In the present investigation, an attempt has been made to isolate, characterize and screen the Tulsi (Ocimum sanctum Linn.) root fungal endophytic fractions (TRF) for hepatoprotective and antioxidant activities. Endophytic fungi from Ocimum sanctum Linn. roots were isolated and cultured aseptically in PDA media. The full fledged grown fungus cultures were fermented in potato dextrose broth and fractionated using ethyl acetate. TRF-1 and TRF-2 were subjected free radical scavenging activities against 2,2-diphenyl-1-picrylhydrazyl, hydroxyl free radicals and reducing power assay. TRF-1 was found to be potential free radical scavenger with $IC_{50}$ values of $71.83{mu}g/ml$ for DPPH and $110.85{mu}g/ml$ for hydroxyl radical respectively. TRF-1 and TRF-2 were further assessed for hepatoprotective activity in $CCl_4$ induced hepatotoxicity in-vivo. Results showed that TRF-1 (200 mg/kg p.o.) and TRF-2 (200 mg/kg p.o.) significantly reversed the actions of carbon tetrachloride induced hepatotoxicity, as evident by restoration of serum AST, ALT, ALP, bilirubin, triglycerides and protein level to normal values as compared to $CCl_4$ treated group. Restoration of altered LPO (p<0.001), GSH (p<0.01) and catalase (p<0.01) by TRF-1 suggests that the hepatoprotective activity may be attributed to its antioxidant action. This was further supported by histopathological studies. TRF-1 was subjected to rDNA sequencing studies by PCR technique. Based on the morphological and molecular characterization, the fungus was identified as Paecilomyces variotti Bain. Therefore, endophytes from medicinal plants represent great potential for the discovery of new pharmacologically active metabolites.