This research investigated the effect of guide vanes into the intake runner of a diesel engine run with higher viscous biodiesel to enhance the in-cylinder intake airflow characteristics. First, simulation of an internal combustion engine base model was done. Guide vanes of various lengths were developed and imposed into the intake runner to investigate the airflow characteristics. Based on the simulation results, five guide vanes models of 8, 10, 12, 14, and 16 mm length were constructed and tested on a compression ignition (CI) engine run with biodiesel. According to the experimental results of engine performance and emissions, it was found that guide vanes of 12 mm length showed the highest number of improvements with 14 mm and 10 mm length showed the second and third highest number of improvements, respectively. Therefore, this research concluded that guide vanes successfully improved the in-cylinder air flow characteristics to improve the mixing of higher viscous biodiesel with air resulting in better performances of the engines than without vanes.