BackgroundGuidelines recommend measuring temperature in children presenting with fever using electronic axillary or tympanic thermometers. Non-contact thermometry offers advantages, yet has not been tested against recommended methods in primary care.AimTo compare two different non-contact infrared thermometers (NCITs) to axillary and tympanic thermometers in children aged ≤5 years visiting their GP with an acute illness.Design and settingMethod comparison study with nested qualitative component.MethodTemperature measurements were taken with electronic axillary (Welch Allyn SureTemp®), electronic tympanic (Braun Thermoscan®), NCIT Thermofocus® 0800, and NCIT Firhealth Forehead. Parents rated acceptability and discomfort. Qualitative interviews explored parents’ experiences of the thermometers.ResultsIn total, 401 children were recruited (median age 1.6 years, 50.62% male). Mean difference between the Thermofocus NCIT and axillary thermometer was −0.14°C (95% confidence interval [CI] = −0.21 to −0.06°C); lower limit of agreement was −1.57°C (95% CI = −1.69 to −1.44°C) and upper limit 1.29°C (95% CI = 1.16 to 1.42°C). A second NCIT (Firhealth) had similar levels of agreement; however, the limits of agreement between tympanic and axillary thermometers were also wide. Parents expressed a preference for the practicality and comfort of NCITs, and were mostly negative about their child’s experience of axillary thermometers. But there was willingness to adopt whichever device was medically recommended.ConclusionIn a primary care paediatric population, temperature measurements with NCITs varied by >1°C compared with axillary and tympanic approaches. But there was also poor agreement between tympanic and axillary thermometers. Since clinical guidelines often rely on specific fever thresholds, clinicians should interpret peripheral thermometer readings with caution and in the context of a holistic assessment of the child.