Abstract Background Understanding the incidence, mortality, disability-adjusted life years (DALYs), years lived with disability (YLDs), and years of life lost (YLLs) due to self-harm and analyzing their trends over time is the first step towards designing an effective suicide prevention strategy. This study aims to investigate the trend of self-harm indicators at the national level and in the provinces of Iran, by gender and age groups. Methods In this ecological study, the trend of self-harm indicators in Iran was examined during the period 1990 to 2021. Data were extracted from the Global Burden of Disease (GBD) database and their secondary analysis was performed with Joinpoint regression using Joinpoint 5.2 software. The spatial pattern of the indices was examined using Hot spot Analysis. The Pearson correlation coefficient was used to evaluate the correlation of indicators with the Socio-demographic index (SDI) in 1990, 2000, 2010, and 2021. Results According to estimates, the incidence, death, DALY, YLDs, and YLLs due to self-harm in Iran decreased over 32 years. On average, the annual incidence rate decreased by 0.72% (AAPC = -0.72), death by 1.39% (AAPC = -1.39), DALY by 1.44% (AAPC = -1.44), YLDs by 2.07% (AAPC = -2.07), and YLLs by 1.41% (AAPC = -1.41). The incidence trend was upward in men (AAPC = 0.25) while it was downward in women (AAPC = -1.38). A downward trend was observed in all age groups, with the greatest decrease observed in the 10–19 age group. In most provinces, the indicators decreased. The largest decrease in incidence and YLDs was observed in Kurdistan Province (AAPC = -1.42 and AAPC = -2.94, respectively) and in the three indicators of death, DALY and YLLs in Chaharmahal and Bakhtiari Province (AAPC = -2.32, AAPC = -2.52 and AAPC = -2.49, respectively). Only in Sistan and Baluchestan Province, the death rate (AAPC = 0.09), DALY (AAPC = 0.18) and YLLs (AAPC = 0.22) increased. In addition, there was a significant relationship between subnational SDIs and YLDs (r = -0.401, P = 0.025) in 2021. Between 1990 and 2021, Kermanshah and Ilam consistently appeared as hot spots for all self-harm indicators. Khuzestan also exhibited significantly elevated values, except for YLD and YLL. Conversely, Qom, South Khorasan, and Semnan were identified as persistent cold spots for mortality, DALYs, and YLL. Conclusion The increasing trend of some indicators in men and some regions such as Sistan and Baluchestan province requires special attention and implementation of targeted intervention programs.