Oil extraction and biodiesel production process produce a massive amount of by-products like Jatropha press cake (JPC) and crude glycerol (CG), which could be used as a potential substrate for methane production. However, the higher lignocellulosic and nitrogen content in the JPC act as a recalcitrant and inhibitor, respectivly, for microbes that are involved in the anaerobic digestion (AD) process. Therefore, the present study aimed to enhance the methane yield of JPC by optimizing the alkaline pretreatment and co-digestion process conditions. The effects of NaOH concentration, incubation temperature, and retention time on methane and soluble chemical oxygen demand (sCOD) yields were evaluated and modeled by employing a response surface methodology coupled with central composite design (RSM-CCD). Moreover, a series of batch experiments with various feedstock concentrations (FCs) were tested to investigate the methane yield of JPC when co-digested with CG at different levels. The methane yields of all pretreated samples were significantly higher when compared with these of the untreated JPC. Pretreating the JPC using 7.32% NaOH at 35.86 °C for 54.05 h was the optimum conditions for maximum methane increment of 40.23% (353.90 mL g−1 VS), while co-digesting 2% CG with JPC at 2 g VS L−1 FC enhanced the methane yield by 28.9% (325.47 mL g−1 VS). Thus, the methane yield of JPC was effectively increased by alkaline pretreatment and co-digesting with CG. However, the alkaline pretreatment was relatively more effective compared with the co-digestion process.