Research on alternatives to rectal thermometry in canine and feline patients has focused on equipment and measurement location but not procedure duration. In a cross-over designed clinical scenario, we evaluated the time prior to and after (Pre-TempT and Post-TempT) rectal and axillary thermometry in canine (n = 114) and feline (n = 72) patients. Equipment duration was controlled for to determine a presumptive total time (TTime) associated with each thermometry method. Pre-TempT and TTime was significantly shorter in axillary thermometry trials for both canine and feline pets (P < 0.001). There was no difference in Post-TempT between thermometry methods in canine patients (P = 0.887) however, the Post-TempT was longer in felines after axillary thermometry (P = 0.004). Reductions in Pre-TempT and TTime were not significant in Scottish Fold breed cats and within the feline rectal trials, the TTime of domestic-long hair breeds was significantly longer than domestic-short hair breeds (P = 0.019). No other tested parameter played a significant role in these results. Axillary thermometry was faster than rectal thermometry in both canine and felines pets due primarily to the time associated with animal approach and restraint (Pre-TempT). These results have implications when optimizing clinic workflow, appointment durations and patient handling time.