Objective  To evaluate the timeliness of infectious diseases reporting in medical institutions in Chongqing before and after the application of Chongqing Infectious Disease Information System.

Methods The reporting cards of infectious diseases in the first half of each year from 2015 to 2024 were selected from 47 medical institutions participating in online reporting of infectious diseases in Shapingba district, Chongqing, for the comparison of the timeliness of infectious disease reporting before and after the application of Chongqing Infectious Disease Information System.

Results In the first half of 2023, the average time needed for one reporting of infectious disease was 10.68 h the median 8.96 h, (P₂₅, P₇₅: 3.64 h,17.87 h). After the application of Chongqing Infectious Disease Information System, the average time was 8.70 h in 2024 the median 5.69 h, ( P₂₅, P₇₅: 1.79 h,15.90 h), a decrease of 1.98 h, and the difference was significant (Z=−33.594, P<0.001). The reporting timeliness was improved by 4.16 h in the primary health care settings averagely and by 1.84 h and 1.75 h, respectively, in the second-and third-level medical institutions averagely. The reporting timeliness was improved by 0.94 h for the infectious diseases in class B and by 2.82 h for the infectious diseases in class C. The improvement in reporting timeliness of infectious diseases in children in child care settings and students were the most obvious, which were shortened by 3.11 h and 2.51 h, repectively.

Conclusion The timeliness of infectious diseases reporting has been improved in Chongqing since the application of Chongqing Infectious Diseases Information System, especially in primary health care settings and in child care settings and schools. It is suggested to promote the application of this system in more medical institutions for the purpose of further improvement of timeliness of infectious disease reporting and the promotion and application of national front-end software.