This study investigates the prevalence, stability, and associated factors of internalizing symptoms in children and adolescents within a clinical setting. The sample included 299 patients aged 3–17 years from a Child and Adolescent Mental Health outpatient clinic, followed over one year. Internalizing symptoms were assessed using the parent-rated version of the Strengths and Difficulties Questionnaire (SDQ), completed at baseline and at one-year follow-up. Stability was evaluated using prospective consistency, retrospective consistency, kappa coefficient, and Spearman’s Rho correlations. Multivariate analyses were conducted to examine associated factors. Baseline prevalence of internalizing symptoms was 40% (95% CI: 33.4-44.8%), with moderate one-year stability (ρ = 0.48, 95% CI: 0.37-0.58). Key factors associated with internalizing symptoms at follow-up included: For girls, higher baseline SDQ emotional symptoms (OR = 2.12, p < 0.001), lower paternal education (OR = 9.70, p = 0.003), and lower SDQ hyperactivity/inattention scores (OR = 0.70, p = 0.016). For boys, comorbid externalizing symptoms (OR = 8.18, p < 0.001), maternal anxiety (OR = 2.35, p = 0.031), maternal unemployment (OR = 2.13, p = 0.043), and a sibling diagnosed with ADHD (OR = 0.10, p = 0.012). For children, peer problems (OR = 1.20, p = 0.02) and the absence of an externalizing diagnosis (OR = 0.33, p = 0.013). For adolescents, lower paternal education (OR = 5.99, p = 0.003), higher SDQ emotional symptoms scores (OR = 13.48, p < 0.001), and female gender. Gender and age differences in associated factors highlight the interplay of neurobiological and social influences. These findings underscore the importance of considering gender and age-specific factors when developing preventive and therapeutic interventions for internalizing symptoms in clinical populations.