The national screening program for permanent bilateral neonatal hearing loss (PBNHL), launched in late 2014, aims to identify children with hearing loss early on in order to limit the harmful consequences of this condition. Our objective was to evaluate the program’s nationwide implementation two years after its launch. The program includes a universal screening phase in maternity wards. In some regions, a follow-up test (Test3) is also performed after discharge from the maternity ward. Children identified as suspected cases then enter a diagnostic phase. Aggregated regional data on births in 2015 and 2016 were used to calculate several national evaluation indicators: coverage rate, refusal rate, positive predictive value (PPV), the rate of children suspected of having SPBN, prevalence, and distribution by severity. The coverage rate increased significantly between 2015 and 2016 (83.3% vs. 93.8%; p<0.001), while screening acceptance was very high as early as 2015 (refusal rate: 0.1%). In 2016, the rate of suspected SPBN decreased significantly after Test 3 (1.4% vs. 0.9%), while the PPV increased (4.7% vs. 7.6%). In 2015, the prevalence of moderate to profound UHS was estimated at 0.9‰ (95% CI [0.8–1.0]); 57% of newborns with a hearing loss >40 decibels have moderate hearing loss, 17% have severe hearing loss, and 26% have profound hearing loss. The national target of 90% coverage after two years of program operation was exceeded. Test3 appears useful for reducing the burden on diagnostic facilities. Improvements in the reporting of diagnostic data will make it possible to confirm the prevalence and distribution by severity of neonatal hearing loss in France.