Chronic exposure to stressful environments can negatively impact cats’ health and welfare, affecting behavioral, autonomic, endocrine and immune function. Cats in shelters can be subject to high levels of environmental threat. Use of low‐stress handling practices has been recommended to improve shelter cat welfare, but data supporting improved outcomes from using low‐stress handling remain limited. Cardiac activity, particularly heart rate variability (HRV), is an indicator of stress and emotional state in humans and non‐human animals. Recent research demonstrates the importance of HRV as an indicator of important body functions associated with stress responsiveness, environmental adaptability, mental and physical health. To date, studies of HRV in cats are limited, involving mainly anaesthetized or restrained cats. Cardiac data used for HRV calculations is determined from an electrocardiogram (ECG), with computer‐based ECG of immobile cats considered the gold standard. Use of ECGs from ambulatory cats using a Holter monitor has been validated, but analysis of the data obtained is expensive and requires specific training for interpretation. We propose a pilot study to test feasibility of obtaining ECG data for HRV analysis from free‐moving cats, using modifications of a readily available, inexpensive ECG monitoring system, and compared with data from a Holter monitor. Our hypothesis is that the two methods of obtaining HRV data will prove comparable. If successful, this readily available, inexpensive, practical method would be beneficial to the field of shelter medicine, and for demonstrating benefits of low‐stress handling approaches and other interventions designed to improve health and welfare of shelter cats.