Background: Accurate evaluation of bone marrow involvement is important for staging and treatment monitoring in pediatric neuroblastoma. This study evaluated flow cytometry for detecting neuroblastoma cells in bone marrow aspirates. Methods: In this prospective exploratory correlative analysis, samples from 28 children were assessed through flow cytometry and cytomorphology; available histopathological and iodine-123 metaiodobenzylguanidine (MIBG) scintigraphy results were compared. Neuroblastoma cells were identified as nucleated CD56+CD45−CD36−CD71− events. Results: Flow cytometry detected neuroblastoma cell populations across a broad quantitative range, including low-level populations. Agreement between flow cytometry and cytomorphology was 90.0% (Cohen’s κ = 0.56). In 16 paired aspirate-level records with at least one positive result, flow cytometric and cytomorphological percentages showed a positive Pearson correlation (r = 0.878, p < 0.0001), although this association was sensitive to one high-value observation. Agreement with histopathology was 92.1–94.8% (κ = 0.59–0.64), whereas agreement with MIBG scintigraphy was slight to fair (κ = 0.12–0.23). Conclusions: Flow cytometry provided rapid, quantitative detection of neuroblastoma cell populations in bone marrow aspirates. It should be considered complementary to cytomorphology and histopathology, as repeated examinations, the limited panel, and the lack of an independent reference standard preclude definitive estimates of diagnostic performance.