Transthoracic echocardiogram (TTE) is commonly used to screen for pulmonary hypertension (PHTN) in neonates and young infants. However, in the absence of sufficient tricuspid regurgitation (TR), a ventricular septal defect (VSD), or a patent ductus arteriosus (PDA), the estimation of systolic pulmonary artery pressure (SPAP) becomes challenging. Pulmonary artery acceleration time (PAAT) is an alternate parameter that is easy to obtain in almost all patients and does not require the presence of tricuspid valvar regurgitation or an anatomical cardiac defect. We sought to examine the correlation of PAAT with estimated SPAP by TTE and create an equation to estimate the SPAP using PAAT. We performed a retrospective review of TTEs performed on neonates and young infants (4 months of age or younger) at our institution between April 2017 and December 2018, along with the corresponding medical records. We included TTEs that provided estimation for SPAP and at least one PAAT measurement. During the study period, 138 TTEs performed on 82 patients met the inclusion criteria. Strong correlation was delineated between PAAT and SPAP estimated by the maximum velocity of tricuspid valve regurgitation Doppler, correlation coefficient (r) = − 0.83. Moderate correlation was detected between PAAT and SPAP estimated by PDA Doppler, r = − 0.66. Utilizing the following equation “SPAP = 82.6 − 0.58 × PAAT + RA mean pressure”, PAAT can be used to estimate SPAP in neonates and young infants. PAAT can be used as an alternative to TR jet to assess SPAP when the latter is absent or insufficient. Further studies are needed to verify the accuracy of this equation.