The aim of this study was to evaluate the accuracy, invasiveness and impact on clinical results of a digital oral impression protocol in the pre-surgical orthopedic treatment (PSOT) of newborn cleft lip and palate (CLP) patients undergoing primary alveolar surgical repair. Six patients were divided, according to impression technique used, into a digital (intraoral scanner (IOS)) and a non-digital (tray and putty (T&P)) group. Parents considered IOS impressions to be less invasive, compared to T&P impressions. The clinician that took all the impressions considered the IOS to be less stressful compared to the T&P method. In two T&P patients, the impression was repeated because some important anatomical details were missing, in one case due to patient regurgitation during the first attempt. No impression was repeated, and any adverse event was reported in the IOS group. There were no significant differences between these two protocols in pre-surgical alveolar gap reduction and surgical challenge. The study results indicate that this digital protocol can accelerate the production process of the passive molding plate with an instantaneous transmission of the digital impression to the dental lab, maintaining the same accuracy level and clinical outcomes of classical techniques and reducing the invasiveness of impression taking, avoiding any risk of impression material ingestion or inhalation.