The aim of this study was to explore the potentially different associations between two common aspects of adolescents’ life, namely social jetlag and weekend catch-up sleep, with well-being and physical health, according to the actual sleep duration, i.e., <7 h and ≥7 h. To this end, 504 participants (42.1% males), with a mean age of 16.17 (standard deviation = 1.39), were examined in the this cross-sectional study. Participants were asked to wear the Micro Motionlogger Watch actigraph (Ambulatory Monitoring, Inc., Ardlsey, NY, USA) around their non-dominant wrist for seven consecutive days in order to objectively assess social jetlag and weekend catch-up sleep. Participants were also asked to fill in the Mental Health Continuum—Short Form for the assessment of subjective, social, and psychological well-being, as well as the SF-36 Health Survey for the perception of physical health. In adolescents sleeping less than 7 h, those experiencing weekend catch-up sleep longer than 120 min reported significantly lower subjective well-being compared to those with a weekend catch-up sleep duration between 0 and 59 min. These data pointed out the detrimental effect of long weekend catch-up sleep on self-reported well-being only in adolescents getting less than the recommended amount of sleep.