Background Cardiac autonomic neuropathy (CAN) is the most underdiagnosed consequence of diabetes because standard hospital settings do not provide consistent diagnostic criteria or testing resources. It is still unclear how diabetic peripheral neuropathy (DPN) and CAN are related. Therefore, this study aimed to determine the prevalence of CAN in individuals with type 2 diabetes mellitus who had isolated DPN without other microvascular or macrovascular complications. Methodology A total of 35 type 2 diabetes mellitus patients with isolated DPN (group 1) and an equal number of sex- and age-matched patients without DPN (group 2) underwent CAN testing. Results were compared between the two groups. Results A significantly higher prevalence of isolated parasympathetic (28.57 vs. 11.42%), isolated sympathetic (22.85 vs. 8.57%), and combined autonomic dysfunction (37.14 vs. 2.85%) was found in the neuropathic group compared to the non-neuropathic group. Group 1 exhibited more abnormal parasympathetic nervous system test results and increased diastolic pressure during sustained handgrip compared to group 2 (all p-values <0.05). Conclusions A significantly higher prevalence of cardiac autonomic dysfunction is seen in patients with DPN without other microvascular or macrovascular complications, irrespective of age, sex, or duration of diabetes mellitus. Patients with a higher body mass index were found to have significantly increased cardiac autonomic dysfunction.