Background: Ischemic stroke is one of the major causes of disability and mortality. Its effects on the autonomic nervous system (ANS) through nonlinear heart rate variability (HRV) and pulse transit time (PTT) have not been well explored among Thai patients. Objective: This study aims to demonstrate the association between ANS and ischemic stroke through nonlinear HRV and PTT. Methods: In total, 111 patients were enrolled in the study and their short-term HRV and PTT data were collected. Results: Parasympathetic tone was higher in elderly patients (≥60 years). The elderly patients had a higher SD1 but lower SD2 and SD2/SD1 than the younger patients, and a similar pattern was found in the female patients compared to the male patients. These findings were supported by the results of the Poincaré plots. Older and female patients had circular plots and approximately round plots, respectively. Moreover, the parasympathetic nervous system (PNS) response was moderate and positively associated with SD1 (r = 0.47, p < 0.001) and PTT (r = 0.29, p = 0.002), and negatively associated with SD2 and SD2/SD1 (r = −0.47, p < 0.001), after controlling for age and sex. Conclusions: The PNS response was predominant in older and female patients whereas the sympathetic response was lower than in the younger and male patients, which reflected certain characteristics of ANS response to ischemic stroke. Moreover, nonlinear parameters of SD1, SD2, SD2/SD1, and Poincaré plots including PTT are useful and recommended in investigating ANS, particularly in PNS, among ischemic stroke patients.