Nigella sativa is one such plant species indigenous to Middle-east, Eastern Europe, and the Asian Subcontinent. Black cumin seeds derived from N. sativa are one of the identified biomasses to produce biodiesels for the use in an unmodified CI engine. The current study aims to evaluate the credibility of Nigella sativa methyl ester (NSME) as a suitable blend alongside mineral diesel in a common rail direct Injection engine via fundamental combustion analysis. In the present work, 20% of Nigella sativa methyl ester has been tested in diesel engine at 600 bar injection pressure under different pilot and main injection forms. The pilot injection mass has been varied from 5–15% along with variation in main injection also. An optimized injection strategy has been found with respect to performance and emissions for effective implementation of EGR at 10% and 20% rate. At 5% pilot injection, the NSME20 fuel showed comparable brake thermal efficiency and brake-specific fuel consumption at all engine loads. Furthermore, NOx emission of NSME20 fuel has been reduced by increasing the pilot injection rate when compared to diesel and this has been further reduced with 10–20% exhaust gas recirculation. On the other hand, the combustion characteristics of NSME20 blend also shown similar pattern like diesel fuel with slight reduction in cylinder pressure and heat release rate. Finally, it has been concluded that the newly developed Nigella sativa methyl ester can be used as sustainable biofuel for various energy applications in the present scenario.