Delayed diagnosis of HIV can lead to an inappropriate response to antiretroviral therapy (ART), rapid progression of the disease, and death. It can also carry harmful effects on public health due to the increment of transmission. This study aimed to estimate the duration of delayed diagnosis (DDD) in HIV patients in Iran. This hybrid cross-sectional cohort study was conducted on the national HIV surveillance system database (HSSD). Linear mixed effect models with random intercept, random slope, and both were used to estimate the parameters required for the CD4 depletion model to determine the best-fitted model for DDD, stratified by the route of transmission, gender, and age group. The DDD was estimated in 11,373 patients including 4,762 (41.87%) injection drug users (IDUs), 512 (4.5%) men who had sexual contact with men (MSM), 3,762 (33.08%) patients with heterosexual contacts, and 2,337 (20.55%) patients who were infected through other routes of HIV transmission. The total mean DDD was 8.41 ± 5.97 years. The mean DDD was 7.24 ± 0.08 and 9.43 ± 6.83 years in male and female IDUs, respectively. In the heterosexual contact group, DDD was obtained as 8.60 ± 6.43 years in male patients and 9.49 ± 7.17 years in female patients. It was also estimated as 9.37 ± 7.30 years in the MSM group. Furthermore, patients infected through other transmission routes were found with a DDD of 7.90 ± 6.74 years for male patients and a DDD of 7.87 ± 5.87 years for female patients. A simple CD4 depletion model analysis is represented, which incorporates a pre-estimation step to determine the best-fitted linear mixed model for calculating the parameters required for the CD4 depletion model. Considering such a noticeably high HIV diagnostic delay, especially in older adults, MSM, and heterosexual contact groups, regular periodic screening is required to reduce the DDD.