Startle is a fast response elicited by sudden acoustic, tactile, or visual stimuli in a variety of animals and in humans. As the magnitude of startle response can be modulated by external and internal variables, it can be a useful tool to study reaction to stress. Our study evaluated whether acupuncture can change cardiac autonomic modulation (heart rate variability); and behavioural (reactivity) and endocrine (cortisol levels) parameters in response to startle. Brazilian Sport horses (n = 6) were subjected to a model of startle in which an umbrella was abruptly opened near the horse. Before startle, the horses were subjected to a 20-minute session of acupuncture in acupoints GV1, HT7, GV20, and BL52 (ACUP) and in nonpoints (NP) or left undisturbed (CTL). For analysis of the heart rate variability, ultrashort-term (64 s) heart rate series were interpolated (4 Hz) and divided into 256-point segments and the spectra integrated into low (LF; 0.01–0.07 Hz; index of sympathetic modulation) and high (HF; 0.07–0.50 Hz; index of parasympathetic modulation) frequency bands. Acupuncture (ACUP) changed the sympathovagal balance with a shift towards parasympathetic modulation, reducing the prompt startle-induced increase in LF/HF and reducing cortisol levels 30 min after startle. However, acupuncture elicited no changes in behavioural parameters.