Despite extensive research on the psychological impacts of digital technology, the nuanced dynamics between adolescent loneliness and problematic smartphone use, particularly across different educational levels and genders, remain underexplored. This study aims to fill this gap by employing a Random Intercept Cross-Lagged Panel Model to dissect the bidirectional relationship between loneliness and problematic smartphone use among adolescents, with a focus on the moderating roles of educational levels and gender. Engaging 3132 students from various educational institutions in China, the research conducted a three-wave longitudinal analysis across 2022–2023. The final number of participants included 1120 adolescents (53.5% female; age in 2022: M = 14.57 years, SD = 1.57). Results reveal that loneliness significantly predicts problematic smartphone use, but not vice versa, highlighting a unidirectional influence. The study uncovers crucial differences across educational levels and gender, emphasizing the stronger effect of loneliness on problematic smartphone use among junior high students and female adolescents. These findings underscore the complexity of adolescent loneliness and its relationship with digital behavior, suggesting a need for tailored interventions considering both gender and developmental stages.