The study assessed health literacy (HL) in Lebanese adolescents and its associations with health during the COVID-19 pandemic. A sample of 228 adolescents (63.1% female), 15.5 ± 1.5 years, took the survey. Data was collected between May and September 2020. The questionnaire consisted of the Health Literacy for School-Aged Children (HLSAC) scale, the Generalized Anxiety Disorder (GAD-7) assessment, sociodemographic characteristics, and health-related variables. Around 84.6% had low to moderate HL. Adolescents with moderate HL were more likely to spend more than 2 hours on sedentary behavior (OR = 0.3, 95% CI [0.1, 0.9]) and smoke (OR = 0.3, 95% CI [0.1, 0.8]). Adolescents with high HL had lower odds of having moderate to severe anxiety (OR = 0.2, 95% CI [0.1, 0.8]) and excess body weight (OR = 0.1, 95% CI [0.4, 0.5]). Adolescents with high HL had higher odds of having good to excellent health (OR = 1.2, 95% CI [0.4, 3.7]). Interventions to strengthen HL must be implemented with a focus on at-risk adolescents.