A method to calculate the Natural frequency of the Timing belt drive is developed and validated. Timing belt drives are widely used in the automotive engines for valve actuation drives where accurate motion and force transmission is utmost necessary. Natural frequency is an important parameter to understand the vibration behavior of a system. Previous studies have found the Natural frequency and frequency response of the timing belt with experimental method and with FEA/ MBD software. In this study attempt has been made to develop a tool which will require basic material properties to calculate the natural frequency.Complete timing belt drive system is divided into set of standard components/elements. The belt tooth is divided in four layers and stiffness calculation is based on apparent modulus of elasticity derived from form factor. For belt pulley tooth analogy with cantilever beam is used. The model can be used for trapezoidal shaped timing belt as well as for other forms of the tooth. The belt drive level mathematical model is developed by calculating the equivalent system properties from the individual element properties. In order to reduce computational efforts a MATLAB based tool is developed. The validation is done by comparing the mathematical model with the experimental data. The predicted value from the mathematical model and experimental values are in close agreement.