Ultrasound analysis of the diaphragm can provide valuable insights into diaphragmatic function in neonates, potentially enabling physicians to identify disease-related abnormalities. We propose and evaluate an integrated semi-automated video analysis system for the accurate diaphragmatic motion analysis in neonates. In order to enhance the clinical learning outcome and precisely assess the suggested system, we employed 20 simulated ultrasound videos of the diaphragm that were produced using characteristics of typical neonate’s diaphragmatic motion. To evaluate the proposed system, manual (performed by a doctor) vs automated measurements were extracted and diaphragmatic excursion (DE), inspiration time (Tinsp), total breathing time (Ttot), diaphragmatic curve slope (DSP), and relaxation rate (RR) were measured. The following manual (–/) vs semi-automated (/–), (median ± IQR) measurements were computed for all simulated videos; The correlation coefficient (ρ, p-value) are also given showing the correlation of the parameters measured by the doctor vs the proposed system: (i) DE: (3.66 ± 0.11)/3.71 ± 0.24 mm (ρ = 0.97, p = 0.002), (ii) Tinsp: (0.55 ± 0.19)/(0.57 ± 0.16) sec (ρ = 0.91, p = 0.002), (iii) Ttot: (1.31 ± 0.19)/(1.31 ± 0.18) sec (ρ = 0.90, p = 0.005), (iv) DSC: 6.69 ± 2.73/6.58 ± 2.31 mm/sec (ρ = 0.79, p = 0.003), (v) RR: 4.88 ± 0.15/5.08 ± 0.57 mm/sec (ρ = 0.89, p = 0.001). This is the first study reported in the literature that utilizes a semi-automated integrated motion analysis system to assess diaphragmatic motion parameters in neonate simulation videos. No statistically significant differences were found between manual and semi-automated measurements. Therefore, the proposed technique could be helpful for the clinical evaluation of neonate’s diaphragmatic motion. Real ultrasound videos of neonate diaphragms in both normal and pathological motion will be used for additional research and validation on a larger sample.