Objective: This study aimed to investigate the association between stunting and suspected developmental delay status in Kabupaten Bogor. Methods: An observational cross-sectional study was conducted in Puskesmas Kecamatan Ciampea, Kabupaten Bogor, Indonesia, from February to April 2019. We included children aged 6–59 mo who visited outpatient clinics. All eligible children underwent standardized anthropometric examinations and developmental milestone assessments using the Denver II tool. Both bivariate and multivariate analyses were conducted to investigate any associations. Results: From 184 children, 76 (41.3%) were stunted and 82 (44.57%) had suspected developmental delays, both relatively higher than the national prevalence. Overall, developmental delays were associated with stunting (64.5% vs. 30.6%; adjusted odds ratio (AOR): 3.45; 95% CI: 1.76–6.76; p = 0.000). In subgroup analyses, stunting was independently associated with suspected delays in fine motor skills (26.3% vs. 12.9%; AOR: 2.49; 95% CI: 1.00–6.18; p = 0.049), personal‑social development (35.5% vs. 12.0%; AOR: 2.75; 95% CI: 1.24–6.12; p = 0.013) and language skills (27.6% vs. 12.9%; AOR: 2.95; 95% CI: 1.28–6.77; p = 0.011) after multivariate analyses with sex, age and undernutrition as confounding factors in the final model. Conclusion: Stunting had a strong association with developmental delays among children visiting primary healthcare clinics. Stakeholders should focus on both the detection and prevention of stunting and developmental delays in primary healthcare facilities.