Obesity can induce cardiovascular diseases in both humans and animals. Heart rate variability (HRV) is an indicator of sympathovagal balance and is used to identify cardiovascular diseases in humans. However, HRV and cardiac function have rarely been investigated in obese dogs. This study investigated the effect of obesity on oxidative stress, HRV, and cardiac function in obese and non-obese dogs. The nine-scale body condition score (BCS) system was used to determine obesity. Thirty small breed dogs were divided into a normal weight group (n = 15) and an obese group (n = 15). All dogs underwent physical examination, plasma malondialdehyde (MDA) measurement, electrocardiography, echocardiography, and two hours of Holter monitoring. This study found that obese dogs had increased plasma MDA and sympathovagal imbalance, which was indicated by impaired time and frequency domains compared to normal weight dogs. Although cardiac function was within normal limits, the echocardiographic study found that the obese dogs had reduced cardiac wall thickness and lower systolic function, as indicated by a reduction in %ejection fraction, %fractional shortening, increased left ventricular (LV) internal diameter during systole, and LV end-systolic volume compared to normal weight dogs. This study concluded that obesity in dogs can induce increased plasma oxidative stress, impaired HRV, and reduced cardiac systolic function compared to non-obese dogs.