The thymus plays a critical role in the adaptive immune system as the site of T cells maturation. Unfortunately, the thymus is susceptible to damage by acute insults which can negatively impact patient health outcomes. Despite significant medical interest, research into the thymus has been limited due to a lack of intravital imaging methods to study the thymus in situ.Our lab previously developed a method of intravital adhesive-stabilized two-photon microscopy of the thymus in mice to overcome the limitations of previous imaging methods. However, this method was limited by the permanent attachment of a support structure to the thymus, which prevented repeat imaging of the same thymus across multiple timepoints.To enable longitudinal study of the thymus, we developed a vacuum-stabilized video-rate two-photon endoscope capable of imaging the native thymus in mice. The optical performance and ability of the endoscope to visualize the thymus was described. The stability of the endoscope to visualize the thymus was also described. Future longitudinal examination of the thymus is likely to expand the scientific communities' understanding of thymus biology and its relationship to overall human health.