Bone marrow (BM) sampling guidelines in the evaluation of childhood aplastic anemia (AA) and staging neuroblastomas (NB) are sporadically published in the literature. We aim to the present a retrospective audit on the efficacy of BM sampling in above two diagnoses at our centre. Particle squash smears from BM aspirate (BMA), trephine biopsy (BMBx) touch imprint (BMI) smears, and pre-processing BMBx core length (PBCL) were analysed from cases (< 18 years) of AA and NB diagnosed over last 4 years (2019–2022). Fifty-one AA [median age; 9 years, (2–17)] and 25 NB [1 year (0.7–12)] had median PBCL of 18 (10–40) and 10 (5–25) mm, respectively. BMA, BMI, and BMBx had a higher degree of concordance in stratification of AA (Kohen κ; 0.890–1.000, p = 0.0001) and marrow involvement by NB (κ; 0.610, p < 0.001). The PBCL had positive correlation with age (Spearman r; 0.177, p = 0.213) and number of evaluable marrow spaces (r; 0.551, p = 0.000) in AA. PBCL of 11 mm and 08 mm were optimal in the evaluation of AA (AUC; 0.59, sensitivity; 86.3%, specificity; 75%) and NB (0.673, 61.5%, 75%), respectively. Combination of bone marrow aspirate, trephine touch imprint, and ≥ 08 mm of BMBx are satisfactory in the adequate evaluation of AA and staging NB in children and adolescents.