Electromagnetic field (EMF) technology has the potential to improve scientific data capture and welfare assessment by allowing automated data collection from individual cages. However, it is important to determine any impact that a new technology itself may have on animal welfare, and previous studies have found contrasting results of EMF on laboratory rodent anxiety-like behaviour and cognition. We therefore investigated whether there was an effect of low frequency EMF experienced continuously over a six-week period, as an integral part of the animal housing system, on measures of mouse anxiety-related behaviour, cognition and welfare. We housed mice (N = 80) of two strains (BALB/cAnNCrl and C57BL/6NCrl) separately in Individually Ventilated Cages (IVCs) in groups of four, either with the EMF plate turned 'on' or 'off' (n = 5). Some measures, e.g. food and water utilisation, were collected at regular intervals, whereas measures of anxiety-like behaviour (e.g. open field test) and cognitive performance (novel-object recognition test) were collected only at the end of the study. We found expected strong strain differences in most measures, e.g. latency to leave the starting square in an open field test, with C57BL/6NCrl mice moving away sooner, and interactions between strain and time for those measures recorded at more than one time point, e.g. significant weight gain over time for both strains, but with BALB/cAnNCrl mice weighing more. However, we found no significant effects of treatment (EMF 'on'/'off') for any of the measures collected. These results indicate that, for the measures recorded here, there was no measurable impact on the behaviour and welfare of low frequency EMF exposure experienced continuously over a six-week period. Housing systems that include EMF monitoring technology may therefore be suitable for use without influencing either animal welfare or scientific outcomes.