Use of alternate access for complex neonatal interventions has gained acceptance with carotid and axillary artery access being used for ductal and aortic interventions. This study was a retrospective, single-center study at Cincinnati Children's Hospital Medical Center. The study included infants, aged ≤90 days, who underwent cardiac catheterization with either carotid or axillary artery access between 2013 and 2022. Data encompassing demographics, clinical information, catheterization data, and the incidence of pseudoaneurysm as a procedural complication were collected. Among 29 young infants (20 males, 69%), 4 out of 15 patients (27%) who underwent the carotid approach developed pseudoaneurysms, while 1 out of 14 patients (7.1%) who underwent the axillary approach developed one. Two patients required transcatheter intervention due to enlargement of pseudoaneurysms, involving the placement of transarterial flow-diverting stent and occlusion of left common carotid artery. Longer sheath in-to-out time (135 vs. 77 min, p = 0.001), and higher closing activated clotting times (ACT) (268 vs. 197 s, p = 0.021) were observed among patients with pseudoaneurysms compared to those without. Young infants with alternative access via the carotid and axillary arteries may be at risk of pseudoaneurysm formation during longer procedures and with higher ACTs for closure. Ultrasound-guided compression can be employed to prevent the progression and in resolution of these lesions.