Dysfunctional movement, a suggested contributing factor for musculoskeletal pain and injury, appears to increase as adolescents experience puberty. This study investigated dysfunctional movement among a group of ninth-grade physical education students to determine if a standardized functional movement warm-up (FMWU) would improve movement quality more than a regular physical education warm-up. The FMWU group (n = 22) completed the assigned warm-up 3 times/week over 9 weeks, whereas the regular warm-up (RWU) group (n = 22) completed a regular dynamic warm-up. The Functional Movement Screen (FMS) was used in the assessment of movement quality pre and post. The FMS total composite mean score was 12.20 (SD = 1.56). Additionally, 45.5% of participants had at least one asymmetry and 93.2% scored a 1 on at least one FMS task. There was a significant Group × Time interaction, F(1, 42) = 11.27, p = 0.002. The FMWU group significantly improved for the total composite score, deep squat (DS), rotatory stability, and scores of 1. All other measures of movement trended positively for the FMWU group except the inline lunge (ILL), which remained the same. The RWU group slightly or significantly worsened in the DS, ILL, active straight leg raise, and hurdle step, and the total composite score did not change. The findings of this study suggest there is a high rate of dysfunctional movement among ninth-grade adolescents and an intentionally designed FMWU is an efficient method of addressing movement quality in physical education.