The duration and frequency of mobile phone calls, and their relationship with various health effects, have been investigated in our previous cross-sectional study. This 2-year period follow-up study aimed to assess the changes in these variables of same subjects. The study population comprised 532 non-patient adult subjects sampled from the Korean Genome Epidemiology Study. The subjects underwent a medical examination at a hospital in 2012/2013 and revisited the same hospital in 2014/2015 to have the same examination for the characteristics of mobile phone use performed. In addition, to evaluate the effects on health, the Headache Impact Test-6 (HIT-6), Psychosocial Well-being Index-Short Form, Beck Depression Inventory, Korean-Instrumental Activities of Daily Living, Perceived Stress Scale, Pittsburgh Sleep Quality Index, and 12-item Short Form Health Survey were analyzed. For all these tests, the higher the score, the greater the effect on health. Variances between scores in all the indices in the baseline and follow-up surveys were calculated, and correlations of each index were analyzed. The average duration per call and HIT-6 score of the subjects decreased significantly compared with those recorded two years ago. The results showed a slight but significant correlation between call duration changes and HIT-6 score changes for female subjects, but not for males. HIT-6 scores in the follow-up survey significantly decreased compared to those in the baseline survey, but long-time call users (subjects whose call duration was ≥5 minutes in both the baseline and follow-up surveys) had no statistically significant reduction in HIT-6 scores. This study suggests that increased call duration is a greater risk factor for increases in headache than any other type of adverse health effect, and that this effect can be chronic.