We aimed to assess whether high school students’ sleep quality, mental health and learning changed during the COVID-19 pandemic as adolescents transitioned from learning online back to studying in person. We conducted an anonymous online cross-sectional survey study at three competitive high schools in Vilnius, Lithuania, after they were reopened. Students provided subjective views on their study quality, their health as well as daily life while studying either virtually or in person and completed the Beck depression inventory (BDI), the Generalized anxiety scale-7 (GAD-7) and the Pittsburgh sleep quality index (PSQI). Among 628 (70.4% female) respondents, 268 (42.7%), 342 (54.5%) and 398 (63.4%) are suspected to have depression, an anxiety disorder or poor sleep, respectively. Students reported better study quality (Z = −12.435, p < 0.001) and physical health (Z = −9.176, p < 0.001), but worse sleep quality (Z = −19.489, p < 0.001), shorter sleep duration (Z = −19.509, p < 0.001) and worse self-reported mental health (Z = −2.220, p < 0.05) while learning in person. However, higher scores of in-person study quality and physical health were associated with lower depression and anxiety levels as well as better sleep. Our study suggests that the reopening of schools may exacerbate sleep and mental health-related issues among high school students but also be beneficial for their academic development and levels of physical activity.