This study compares three selected navigation applications which are Google Maps, Waze and HERE WeGo, through the study of each application’s Application Programming Interface (API). The study is focusing on the aspect of Estimated Time of Arrival (ETA) accuracy, in an attempt to determine which API are suitable to be integrated and implemented in the development of a shuttle bus application. To date, there are currently lacking studies that discuss or compare the implementation of API in the development of shuttle bus tracking and ETA application. This study focuses on finding which API is the best suitable for such development from an ETA perspective, using the navigation application where the APIs were implemented or based on as a tool of testing. An experiment was conducted in a city in Kuala Lumpur, Malaysia, by collecting the ETA of the navigation applications from multiple points while riding a scheduled shuttle bus. The ETA will be compared with actual arrival time (ATA) using RMSE, MAE and PE metric. Comparison results showed Google Maps app provides the most consistent ETA prediction accuracy in a conservative manner and is the most suitable to be incorporated into a simple bus tracking and ETA app. The significant contribution of this study is to provide a result of comparison of the ETA accuracy through selected navigation applications and comparison of their navigation API.