Background: Understanding the university students’ perception of Water Pipe smoking addictions and factors behind the rise in the prevalence of Water Pipe smoking will contribute effectively in the prevention strategies and policies development. Aims: Thus, this study aims to assess the prevalence of Water Pipe smoking among university students and their perceptions on its addiction in Palestine, Jordan, and Turkey, as an initial step to reduce the spread of Water Pipe smoking. Methods: An online self-structured questionnaire was administered to 2030 selected university students from Palestine, Jordan, and Turkey. Prevalence, knowledge and other related factors concerning Water Pipe smoking and its addiction were compared between university students from three Middle East countries (Palestine, Jordan, and Turkey) using SPSS software for statistical analysis. Results: The overall prevalence of Water Pipe smoking was 31.8%, less than a quarter of university students (21.7%) had ever smoked Water Pipe. The highest percentage of current Water Pipe smokers were Palestinians (36.11%), and the lowest percentage was from Turkey (20.23%). Approximately 43% of Water Pipe smokers believe that they will be addicted to Water Pipe smoking and almost half of them smoke Water Pipe daily. The highest percentage of smokers were university students 25 years old and above. However, the highest percentage of smokers was low monthly income students. The university students living with their families were smoking Water Pipe less frequently than students living in private residencies. Conclusions: The prevalence of Water Pipe smoking among university students in Palestine and Jordan was high compared to Turkey. It was believed that the Turkish rules and regulations of Water Pipe smoking limit the Water Pipe smoking in Turkey.