Congenital hypothyroidism (CH) may lead to irreversible mental retardation. To prevent the complication, screening was conducted routinely for all neonates in Iran. This study aimed to evaluate the appropriateness of CH screening programs in Fars province, southern Iran. This retrospective study (February–May, 2017) was conducted in the Health System Research Center of Shiraz University of Medical Sciences (SUMS). The data were obtained from the non-communicable diseases’ unit of SUMS regarding congenital hypothyroidism screening of all neonates born in Fars province from 2005 to 2015. We evaluated the coverage of CH screening, the incidence rate of CH, the percentage of the neonates screened for CH in ideal time, and neonates with CH treated in appropriate time. Descriptive statistics were used to determine the indices. To compare the incidence rate of boys and girls, we used Chi-square test. The coverage of CH screening in Fars Province increased from 50.0% in 2005 to 99.7% in 2015. Furthermore, the percentage of the neonates screened in the ideal time and the neonates with CH treated in an appropriate time increased from 26.0% and 78.0% in 2005 to 86.6% and 99.7% in 2015, respectively. In the evaluated period, the coverage of CH screening in Fars province (98.1%) was higher than that of the other provinces of Iran (83.0%). The study showed good screening coverage in Fars Province from 2005 to 2015. The coverage was considerably better than other provinces of Iran and improved during the study period. Also, over the course of time, more neonates were screened in an ideal time and treated in the appropriate time.