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In reactivity-controlled compression ignition (RCCI) engines, the ignition and combustion of premixed low reactive fuel (LRF) such as natural gas (NG) is controlled by the injection of high reactive fuel (HRF) such as diesel fuel during the compression stroke. In this study, the effects of six different input parameters on the performance and emissions of the natural gas/diesel fueled RCCI engine are studied using fractional factorial design (FFD) method, which is one of the design of experiment (DOE) methods. In this method, the effects of the interactions of input parameters, referred to as “factors,” on the outputs, referred to as “responses,” are investigated. The factors include premixed ratio (PR), start of first injection (SOI1), spray angle (SA), exhaust gas recirculation (EGR), start of second injection (SOI2), and mass fraction of first injection. Sixteen runs were conducted to evaluate the effects of the interaction between input factors on performance and emissions of a RCCI engine using a validated computational fluid dynamics (CFD) model. DOE results indicate that in order to increase gross indicated efficiency (GIE), higher premixed ratio, 85%, with wider spray angle, 150°, is an effective way. Meanwhile, carbon monoxide (CO) and unburned hydrocarbons (UHC) emissions as well as ringing intensity (RI) are decreased at this condition. To reduce NOx emissions, it is beneficial to raise premixed ratio from 55% to 85% or to use 40% EGR, independently.