The risk of venous thromboembolism (VTE) with gender-affirming hormone therapy (GAHT) in transgender and gender non-binary (TNB) youth is unclear. To identify the rate of VTE in a cohort of TNB youth followed in the transgender health clinic at Boston Children's Hospital, and to investigate the impact of congenital thrombophilia diagnosis on the use of GAHT. ICD-9 and ICD-10 codes were used to identify eligible individuals, defined as (i) having a diagnosis of gender dysphoria and (ii) venous thromboembolism (VTE). Data were abstracted from a review of medical records. A second data query assessed TNB individuals who had an associated thrombophilia diagnosis. The primary analysis included 1860 individuals. Total 942 individuals (50.6%) had started GAHT at the time of data analysis. Mean age (±SD) at GAHT initiation was 16.8 (±1.9) years. Five thrombotic events were identified in three (0.13%) individuals, all in the setting of additional VTE risk factors. Only two of five thrombotic events occurred while receiving GAHT. The rate of VTE in the GAHT cohort did not statistically differ from the rate of VTE in the non-GAHT cohort (0.1% vs. 0.2%, p=.62). Of the 10 individuals diagnosed with a congenital thrombophilia, two transmasculine individuals received prophylactic anticoagulation prior to GAHT. No VTE has been reported to date in this cohort. In our cohort, VTE was rare in the TNB youth and was not associated with GAHT use. TNB youth with congenital thrombophilia have not developed VTE in the setting of GAHT use to date.