Effective utilization of biofuels is believed as one of the vital potential sustainable energy resources in current years. Over the last two decades, it has lured the attention of many researchers in the automotive sector to find the solution to problems of global warming, depletion of fossil and fluctuation of fuel prices, and growing reliance on imported energy sources. This experimental investigation aims to assess the impact of graphene nanoparticles (GNP) on the performance and emissions of a compression ignition engine fuel with Jatropha (J20), and Karanja (K20) blends contrasted with that of neat diesel. This research work used a single-cylinder, four-stroke, water-cooled, naturally-aspirated direct injection diesel engine. It was coupled to an eddy current dynamometer with a rated output of 3.5 kW at a speed of 1500 rpm. Samples of GNP in mass fractions of 50 and 100 mg/L were prepared, and their physicochemical properties were evaluated. Measurements were collected to examine the performance and exhaust releases. In addition, the combustion indicators, including in-cylinder pressure, heat release rate, and mean gas temperature, have been studied and analyzed. The experimental result has shown that by adding 50 mg/L GNPs in K20 and J20, the brake thermal efficiency improved by about 4.77%–7.17%, respectively, compared to their base blends. The maximum smoke level was detected to be about 43% at full-load for both biodiesels at 50 mg/L GNP proportion. NO x concentration has also considerably decreased to about 8%–14% for GNP added blends compared to J20 and K20 biodiesel operations. However, a higher proportion of GNP added blends affects the combustion rate and substantial drop in the engine’s performance at maximum load.