Cell phone usage is highly prevalent among young adults. They are used for multiple purposes including communication, studies, social networking and entertainment. However, its excessive usage has been associated with adverse health outcomes. The objective was to find the association of cell phone usage with musculoskeletal discomfort (MSD) and its associated factors. A cross-sectional study was conducted on young adult students from a low-middle income country over a period of 3 months from December 2018 to February 2019. A structured questionnaire based on the Disabilities of the Arm, Shoulder and Hand (QuickDASH scoring) was used to record the musculoskeletal discomfort. Out of 803 questionnaires, data of 754 (94%) were entered and the remaining questionnaires (n = 49) were discarded due to incomplete answers. The mean age was 20.83 (1.62) years. In our study, there were 194 (25.7%) males and 560 (74.3%) female participants. Neck and shoulder were the most frequently affected regions. A significant difference in QuickDASH score was observed between genders (p-value p ≤ 0.001). Left-handed individuals scored significantly higher on QuickDASH score compared to right-handed individuals (p < 0.05). Increased musculoskeletal discomfort was reported by individuals with daily cell phone use of more than four hours (p < 0.05). A positive significant correlation was found between continuous one hour cell-phone use and higher mean QuickDASH scores (correlation coefficient 0.124, p value 0.001). Shorter eye-to-screen distance was significantly associated with MSD (p < 0.05). Musculoskeletal discomfort is associated with the female gender, duration of cell phone use and a small eye-to-screen distance.