Branding horses with permanent marks is still a routine for many breeders in many parts of the world. This method of identification is traditionally done with a hot iron, although cold or freeze branding with liquid nitrogen has been widely disseminated as a less painful method. However, there are no studies comparing freeze and hot iron branding related to horses. This study aimed to compare brand quality and autonomic responses (heart rate variability), cortisol levels, and behavioral responses induced by hot branding (hot iron) and freeze branding (liquid nitrogen). Twenty-three foals of pure and crossbreds of Mangalarga Marchador, aged between 20 and 28 weeks, males and females were branded with the symbol 47 (6.5 × 8.5 cm) on the left shoulder. The animals were divided into 2 groups: hot iron (n = 11) and freeze (n = 12) and the twitching lip method was used to restrain the animals during the branding. No differences in cortisol levels were detected between the 2 groups. In the behavioral assessment, only in the hot iron group was one case of kicking and another of rearing observed. Horses in the hot iron group had more limb movements than did those in the freeze group. Our results have shown that hot iron branding has higher autonomic activation than freeze branding, with sympathetic predominance over the parasympathetic activation, as characterized by higher LF/ HF ratio, LF, SDNN/RMSSD ratio, and lower HF. Freeze branding produced fewer wounds and necrosis in the skin with no significant differences in the sharpness of the mark. Freeze branding proved to be a better option than hot iron because it causes less intense autonomic stress responses and fewer open wounds while giving the same sharpness as the hot iron branding. In terms of animal welfare, hot iron branding should be avoided or universally banned.