Background: Kidney and ureter cancers are two of the most prevalent urological cancers among Iranians. However, studies on the epidemiology and incidence of these cancers are primarily regional and focus on a specific period. Objectives: The present study investigated the trend of the incidence rate of kidney and ureter cancer in Iran from 2004 to 2016. Methods: In this study, information on kidney and ureter cancer cases in Iran from 2004 to 2016 was extracted from the Iranian National Cancer Registry (INCR). Crude and age-specific incidence rates (ASIR) were calculated, and the age-standardized rate (ASR) was measured, using the World Health Organization (WHO) standard population. The Joinpoint software program 4.9.0.1 was used to calculate the annual percent changes (APC) in the trend of the incidence rate of kidney and ureter cancers by age group, regional centers, and tumor grades across a 13-year period. Results: During the study period, 19 659 incidences of ureter and kidney cancer occurred in Iran. The crude and ASR of kidney cancer increased from 0.98 and 1.33 per 100 000 population in 2004 to 3.1 and 3.5 per 100 000 population in 2016, respectively. In addition, the crude and ASR of ureter cancer increased from 0.04 and 0.05 per 100 000 population in 2004 to 0.9 and 1.1 per 100 000 population in 2016, respectively. The national ASR of kidney cancer APC was 22.2% (P > 0.05) from 2004 to 2006 and 4.8% (P < 0.05) from 2006 to 2016, respectively. The national ASR of ureter cancer APC was 290.8% (P < 0.05) from 2004 to 2006 and 7.5% (P < 0.05) from 2006 to 2016. Conclusions: According to the results of this study, the incidence rate of kidney and ureter cancer increased over 13 years in Iran. Hence, the implementation of epidemiological studies in various regions and provinces is crucial for gaining a comprehensive and precise understanding of the underlying causes of kidney and ureter cancer incidence.