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Background There has been an increased emphasis on institutional births, and thus an increasing clinical work load for health care professionals in the recent past. Hence, continuing education, training, ongoing supervision, and mentorship of health care professionals working in these health facilities with easy access to guidelines in a cost effective manner has become a challenging task. With the increased emphasis on institutional births, and an increasing clinical work load, continuing education and training of health care professional managing these health facilities, their ongoing supervision, mentorship, with ready availability of guidelines in a cost effective manner becomes imperative and is a challenging task. Training opportunities can be linked to mobile electronic devices and ‘Apps’ to improve the care of seriously ill newborn. The aim of this study was to evaluate the efficacy of an innovative point of care tool- Android based App- ‘AIIMS-WHO CC STPs’ on the knowledge, skill scores, and satisfaction among Special Newborn Care Unit (SNCU) physicians managing sick neonates. Methods The baseline knowledge and skill scores of pediatricians working in SNCUs in the state of Tamil Nadu, India (n = 32) were assessed by 25 multiple choice questions (MCQs) and by five Objective Structured Clinical Examination (OSCE) skill stations. The training was conducted in a single-day workshop using the app on four modules followed by post-training assessment of knowledge and skill scores after 3 weeks using the same. The satisfaction was assessed by mixed method approach using Likert’s scale and focus group discussion (FGD) after 3 weeks. Results The mean knowledge scores [19.4 (2.6) vs. 10.7 (3.2); maximum marks (MM) 25, mean difference 8.7 (95 % CI 7.6 to 9.9)], and the composite mean skill scores [55.2 (5.8) and 42 (6.2), MM 75, mean difference 13.2 (95 % CI 10.4 to 15.9)] improved after training. The median (IQR) satisfaction score with the course was 4 (4 to 5) (Likert’s scale). Focus group discussion revealed that the physicians were overall satisfied using the device. They expressed overall satisfaction on the teaching methodology using wall charts, simulators, and device. Conclusion Training SNCU physicians on Android based App- ‘AIIMS-WHO CC STPs’ improved their knowledge and skills. This app may have a potential role as a supplement to other modalities in training doctors for improving newborn care.