Background: Juvenile Systemic Lupus Erythematosus (jSLE) is a multisystem inflammatory disease associated with bone loss. However, some patients experience fractures prior to the impairment of bone mineral density (BMD), suggesting that other bone microarchitectural properties, including the Trabecular Bone Score (TBS), may contribute to an increased risk of fragility fractures. Purpose: To assess TBS values in patients diagnosed with jSLE; to compare them with data from an age- and sex-matched sample of healthy individuals; to associate TBS with BMD values; and to evaluate the correlation between TBS and clinical risk factors, fractures, and BMD. Research Design: An observational, analytical, retrospective study. Study Sample: Patients with jSLE aged between 5 and 19 years. Data Collection: Clinical data and BMD values obtained by DXA between 2017 and 2022 at a quaternary care center were analysed. The BMD and TBS data were compared with existing published data from healthy Brazilian children and adolescents after age and sex matching. Results: Ninety-four examinations from 50 jSLE patients were analysed. Twenty-one (22.3%) examinations showed significantly lower TBS values than controls. TBS was lower in female patients aged 14–16 and 17–19 years compared with their peers (1.381 vs 1.466 and 1.397 vs 1.479, respectively). BMD and TBS were concordant in 80/94 (85.1%) examinations, demonstrating a moderate and positive correlation (p < 0.0001). There was no correlation between TBS and previous fractures, disease duration, high disease activity, cumulative glucocorticoid dose, or the presence of fragility fractures. Conclusion: Patients with jSLE exhibited bone microarchitectural impairment, regardless of previous fragility fractures, disease duration, disease activity, or cumulative glucocorticoid exposure.