Dietary supplement users tend to have a better diet quality and overall prudent lifestyle. The main goals of this research were to report the prevalence and type of dietary supplements among Croatian adolescents and to examine the differences in the diet quality among dietary supplement users vs. non-users at the beginning (15/16 y) and at the end of high school education (18/19 y). This research is based on results of the longitudinal CRO-PALS study in which 607 adolescents participated, who had complete dietary, anthropometric, and physical activity data at the beginning (15/16 y) and at the end of their high school education (18/19 y). The dietary assessment method used was a single multi-pass 24 h recall. Dietary supplement users were divided into two groups for the purposes of statistical analysis—users of vitamin and multivitamin preparations (VMV) and users of mineral and multivitamin preparations (MMV). As they aged, there was an increase in the consumption of dietary supplements, and the most frequently used preparation in both age groups was vitamin C (23.7% of users). Dietary supplement users had a higher intake of non-carbonated sweetened drinks and a lower intake of fruits and vegetables in both genders and both age groups. Fast food intake was higher among dietary supplement girl users and boys who were not dietary supplements users in both age groups. Dietary supplement users had a higher achieved average intake of most micronutrients (values obtained only from food) in both genders and both age groups (with exceptions for certain vitamins and minerals). By observing other parameters for assessing the diet quality in this research, we can conclude that girls who do not use dietary supplements have a better diet quality in both age groups.