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Research on alternatives to rectal thermometry in canine and feline patients has focused on equipment and measurement location but not procedure duration. In a crossover clinical scenario, we evaluated the time prior to (Pre-TempT) and after (Post-TempT) rectal and axillary thermometry in a diverse demographic of canine (<i>n</i> = 114) and feline (<i>n</i> = 72) patients. Equipment duration was controlled to determine a presumptive total time (TTime) associated with each thermometry method. Pre-TempT and TTime were significantly shorter in axillary thermometry trials for both canine and feline pets (<i>p</i> < 0.001). There was no difference in Post-TempT between thermometry methods in canine patients (<i>p</i> = 0.887); however, the Post-TempT was longer in felines after axillary thermometry <i>(p</i> = 0.004). Reductions in Pre-TempT and TTime were not significant in Scottish Fold breed cats. Within the feline rectal trials, the TTime of domestic-long-haired breeds was significantly longer than that of domestic-short-haired breeds (<i>p</i> = 0.019). No other tested parameter (i.e., size, body shape, age, weight, breed, coat type, or procedure order) played a significant role in these results. Axillary thermometry was faster than rectal thermometry in both canine and feline pets, primarily due to the time associated with animal approach and restraint (Pre-TempT). These results have implications for optimizing clinic workflow, appointment durations, and patient handling time.