Here, we report on findings from a 15-month follow-up of a school-based program called Empowering a Multimodal Pathway Toward Healthy Youth (EMPATHY). This was primarily intended to reduce suicidal thinking in pre-teens, adolescents, and youth students aged 11–18 in middle schools (Grades 6–8) and high SCHOOLS (Grades 9–12). It also aimed to reduce depression and anxiety. The EMPATHY multimodal program consisted of repeated data collection, identification of a high-risk group, a rapid intervention for this high-risk group including offering supervised online cognitive behavioral therapy (CBT) program, a universal CBT intervention for those in Grades 6–8, a variety of interactions with trained staff (“Resiliency Coaches”), and referral to external medical and psychiatric services where appropriate. There were four time-points at which assessments were made: baseline, 3, 7, and 15 months. Here, we report cross-sectional findings over 15 months in a total of 6,227 students who were assessed at least once during the study period. Additionally, we report longitudinal findings from the 1,884 students who completed all 4 assessments. Our results found highly statistically significant decreases in suicidality rates, with the percentage of the total school population who were actively suicidal decreasing from 4.4% at baseline (n = 143 of 3,244) to 2.8% at 15 months (n = 125 of 4,496) (p < 0.001). There were also highly statistically significant reductions in depression and anxiety scores at each time-point. Thus, Mean Depression scores at baseline for the entire student population were 3.73 ± 3.87 (n = 3,244) at baseline and decreased to 3.22 ± 3.52 (n = 4,496) (p < 0.001). Since most students were not depressed, whole population changes such as this may indicate impact in many areas. In the longitudinal analysis of students who completed all four assessments, there were also highly statistically significant improvements in depression and anxiety scores at all time-points. For example, depression scores decreased from a mean of 3.43 ± 3.67 (n = 1,884) at baseline to 2.95 ± 3.53 (n = 1,884) at 15-months (p < 0.001), while the number who were actively suicidal decreased from 69 to 37. These results suggest that school-based multimodal programs, utilizing a combination of interventions, can have meaningful benefits across entire school populations.