In the current work, an effort is made to study the influence of injection timing (IT) and injection duration (ID) of manifold injected fuels (MIF) in the reactivity controlled compression ignition (RCCI) engine. Compressed natural gas (CNG) and compressed biogas (CBG) are used as the MIF along with diesel and blends of Thevetia Peruviana methyl ester (TPME) are used as the direct injected fuels (DIF). The ITs of the MIF that were studied includes 45°ATDC, 50°ATDC, and 55°ATDC. Also, present study includes impact of various IDs of the MIF such as 3, 6, and 9 ms on RCCI mode of combustion. The complete experimental work is conducted at 75% of rated power. The results show that among the different ITs studied, the D+CNG mixture exhibits higher brake thermal efficiency (BTE), about 29.32% is observed at 50° ATDC IT, which is about 1.77, 3.58, 5.56, 7.51, and 8.54% higher than D+CBG, B20+CNG, B20+CBG, B100+CNG, and B100+CBG fuel combinations. The highest BTE, about 30.25%, is found for the D+CNG fuel combination at 6 ms ID, which is about 1.69, 3.48, 5.32%, 7.24, and 9.16% higher as compared with the D+CBG, B20+CNG, B20+CBG, B100+CNG, and B100+CBG fuel combinations. At all ITs and IDs, higher emissions of nitric oxide (NOx) along with lower emissions of smoke, carbon monoxide (CO), and hydrocarbon (HC) are found for D+CNG mixture as related to other fuel mixtures. At all ITs and IDs, D+CNG gives higher In-cylinder pressure (ICP) and heat release rate (HRR) as compared with other fuel combinations.