Molecular viral load assays are routinely used in high income countries for monitoring the copy number of human immunodeficiency virus (HIV) RNA. However, they require sophisticated facilities and expensive reagents and instruments. Hence, their routine use for patients belonging to resource limited settings is difficult and a low cost alternative is the need of the hour. This was a cross sectional study that analyzed and compared a reverse transcriptase enzyme based assay (Cavidi ExaVir Load version 3) with a real time polymerase chain reaction (PCR) assay (Roche COBAS TaqMan) in resource limited settings with subtype C predominance. The study included 75 HIV-1 positive treatment naïve patients whose CD4+ T lymphocytes count was estimated using BD FACS system and viral loads were quantified using both Cavidi ExaVir Load assay version 3 and Roche COBAS TaqMan Real Time PCR assay. The statistical analysis was performed using the Graph Pad Prism 5 software. The difference in the mean log10 viral load values was found to be 0.2log10copies/ml. The Bland Altman plot showed a clustering of viral load values toward the lower copy range. 78% of the samples had an agreement of ≤0.5 log10 copies/ml and 90.74% of the samples had an agreement of ≤1 log10 copies/ml. Both the assays showed a trend of negative correlation with the CD4+ T cell counts. The study found that ExaVir Load assay can be used as an alternative to the existing molecular assays in resource limited settings for the purpose of routine viral load measurement and monitoring treatment response.