Congenital Cytomegalovirus (cCMV) infection is the leading non-genetic cause of sensorineural hearing loss in newborns. Systematic nationwide screening programs are lacking. Antiviral valganciclovir therapy could improve auditory outcomes if initiated within the first 30 days of life, making timely diagnosis crucial. To address this, we investigated whether a hearing screening-based protocol is suitable. Between 2015 and 2019, newborns ≤21 days of age with repeated abnormal Newborn Hearing Screening (NHS) were prospectively enrolled at University Hospital Frankfurt. Oral mucosal swabs were tested for CMV DNA by real-time PCR, with confirmatory urine and blood-diagnostics in positive cases. Of 2,741 infants presenting for repeat NHS, 2,059 (75.1%) showed normal bilateral findings. Of the 682 (24.9%) with abnormal results, 575 (84.3%) were >21 days and thus ineligible. 107 infants (3.9%) met both criteria — abnormal NHS and age ≤21 days — of whom 100 entered per-protocol analysis. Two (2%) were confirmed cCMV-positive and received valganciclovir. Among the 48 infants who additionally underwent DBS testing, diagnostic sensitivity and specificity were 100%. The presented NHS–driven cCMV protocol reliably identified cCMV-infected newborns timely to offer antiviral therapy. In the absence of universal cCMV screening, this targeted approach offers a challenging, but WHO-screening-criteria-compliant strategy to enable timely antiviral intervention.