Histamine intolerance is a disorder in the homeostasis of histamine due to a reduced intestinal degradation of this amine, mainly caused by diamine oxidase (DAO) enzyme deficiency, which provokes its accumulation in plasma and the appearance of adverse health affects. A new approach for the diagnosis of this intolerance could be the determination of histamine and its metabolites in urine. The aim of this work was to develop and validate a rapid method to determine histamine and methylhistamine in human urine by Ultra High Performance Liquid Chromatography and Fluorimetric detection (UHPLC-FL). The proposed method is a consistent procedure to determine histamine and methylhistamine in less than 11 min with adequate linearity and sensitivity. Relative standard deviation was always lower than 5.5%, ensuring method precision; and mean recovery was greater than 99% for both analytes. The structure of histamine and methylhistamine conjugated with OPA were confirmed by UHPLC-ITD-FTMS which enabled to unequivocally identify both analytes in standards and also in urine samples. The analysis of histamine and methylhistamine in urine samples could be a potential new approach for the routine diagnosis of histamine intolerance, more patient-friendly and with clear advantages in terms of equipment and personnel demand for sample collection in comparison with current plasmatic DAO activity determination.