Accelerator-based boron neutron capture therapy (AB-BNCT) systems are becoming commercially available and are expected to be widely used in hospitals. To ensure the safety of BNCT, establishing a quality assurance (QA) program and properly managing the stability of the system are necessary. In particular, a high level of beam output stability is required to avoid accidents because beam output is a major factor in patient dose. However, no studies have analyzed the long-term beam output stability of AB-BNCT systems. This study aimed to retrospectively analyze the long-term stability of the beam output by statistical process control (SPC) based on the QA results over 3 years. The data analyzed are the results of daily QA (DQA) and weekly QA (WQA) in an AB-BNCT system and were taken between June 2020 and September 2023. The evaluation of the stability of the beam output was based on the reaction rate between gold and neutrons calculated using the activation foil method using a gold foil. In DQA, which can be performed in a short time, the gold foil was applied directly to the beam irradiation aperture in air. In WQA, measurements were performed at the phantom surface, 2-cm depth, and 6-cm depth using a dedicated water phantom. The acquired data were retrospectively analyzed by individuals and a moving range chart (I-MR chart), exponentially weighted moving average control chart (EWMA chart), and several process capability indexes (PCIs). Over 99% of the DQA I-MR chart results were within control limits, whereas the WQA I-MR chart results showed that 1.8%, 4.1%, and 2.0% of the measurements exceeded the control limits at the surface, 2-cm depth, and 6-cm depth, respectively. The variation in the reaction rate of the gold foil before and after the replacement of the target was<0.5%. The EWMA chart results revealed no significant beam output drift for either DQA or WQA. Most measured data were normal based on the results of the Anderson-Darling test and met the requirements for PCI evaluation; most PCI values were>1.0; however, the Cpmk of DQA and the 2- and 6-cm depth WQAs between August 2021 and November 2022 in treatment course 2 were 0.83, 0.77, and 0.87, respectively, which were<1.0. The long-term stability of beam output was confirmed using SPC in an AB-BNCT system. The results of the control chart revealed no significant variation or drift in the beam output, and the quantitative evaluation using PCI revealed high stability. A routine QA program will enable us to provide safe BNCT.