With large-scale Cyber-Physical Systems (Internet of Things) deployments, the low-cost networked devices are becoming ubiquitous. Time stamping of events is a basic requirement and it is crucial for distributed/isolated systems/devices to work in unison. The system clocks of these devices are not very stable and their behaviour is affected by ageing and environmental conditions. A clock’s timing behaviour is generally analysed independently by comparison to a highly stable standard reference clock using specialized instruments. Network Time Protocol (NTP) is widely used for time synchronization over computer networks. As the NTP server clock is more stable in comparison to a client’s system clock, the variation in the end device’s clock offset values with respect to the NTP server clock over a long time can be considered for analysing the behaviour of the end device’s clock. This paper presents a method for analysing clock behaviour based on NTP messages. A computer programme is developed, which utilizes an open-source NTP client library to exchange NTP messages and records end device’s system clock’s offset variations over time for a given periodicity to analyse the behaviour. This black box analysis approach does not require any direct access to the end device’s clock circuit. The solution may be useful for analysing clock behaviour for long-term stability under actual environmental conditions, for deciding time synchronization periodicity to optimize the number of synchronization packet exchanges, and for pre-deployment timing stability assessment of devices for deployment scenarios having intermittent/non-availability of periodic time synchronization.