Reduction of fossil fuel reserves, environmental deterioration, global warming, and rigorous emission norms have necessitated the need for alternate fuel such as biodiesels. Diesel engines produce a higher vibration which leads to a reduced engine life span. In the present study, the vibration of a compression ignition engine has been measured for both diesel and Neem methyl ester. The experiments were carried out at 0%, 25%, 50%, 75%, and 100% load when the engine runs at a constant speed of 1500 rpm and with a compression ratio of 16. Triaxial accelerometer is used for measuring engine vibration along vertical, lateral, and longitudinal directions. Data acquisition and analysis are obtained by NI LabVIEW. It has been observed that an engine running with NME produces lower combustion induced vibration acceleration compared to diesel fuel. It is also noticed that higher peak amplitudes are observed at the frequency of 25 Hz for both diesel and NME, within the range of 0-100 Hz and along three directions. Within the range of 100-3000 Hz, the highest peak amplitudes are observed for engine running with diesel compared to neem methyl ester. At a 100% load, the change in vibration amplitude is 64.94 %, 86.41%, and 17% along vertical, lateral, and longitudinal directions when fuel is changed from NME to diesel. Combustion characteristics such as maximum cylinder pressure, heat release rate, and rate of pressure rise are also measured for both diesel and NME in order to find the relationship between combustion and vibration. At full load conditions, the maximum combustion pressure and maximum rate of pressure rise are increased by 2.1% and 8.33% with pure diesel compared to neem methyl ester. The experimental work suggests that neem methyl ester can be directly used in diesel engines in view of a lesser engine vibration and higher engine life.