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Adolescence is often a period of onset for internalizing and externalizing problems. At the same time, adolescent maturation and increasing autonomy from parents push for changes in family functioning. Even though theoretically expected links among the changes in family functioning and adolescent internalizing and externalizing problems exist, studies examining this link on the within-family level are lacking. This longitudinal, pre-registered, and open-science study, examined the within-family dynamic longitudinal associations among family functioning, and internalizing and externalizing problems. Greek adolescents (N = 480, M age  = 15.73, 47.9% girls, at Wave 1) completed self-report questionnaires, three times in 12 months. Random-Intercept Cross-Lagged Panel Models (RI-CLPM) were applied; such models explicitly disentangle between-family differences from within-family processes, thereby offering a more stringent examination of within-family hypotheses. Results showed that family functioning was not significantly associated with internalizing or externalizing problems, on the within-family level. Also, alternative standard Cross-Lagged Panel Models (CLPM) were applied; such models have been recently criticized for failing to explicitly disentangle between-family variance from within-family variance, but they have been the standard approach to investigating questions of temporal ordering. Results from these analyses offered evidence that adolescents with higher internalizing and externalizing problems compared to their peers, tended to be those who later experienced worse family functioning, but not vice versa. Implications for theory and practice are discussed.