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Abstract The etiology of temporomandibular disorders (TMD), which are considered as a heterogeneous group of psychophysiological disturbances, remains a controversial issue in clinical dentistry. This study aimed to evaluate whether the salivary alpha-amylase (sAA), cortisol levels, and anxiety symptoms differ between children with and without TMD. Initially, 316 young subjects were screened in public schools (nonreferred sample); 76 subjects aged 7–14 years were selected and comprised the TMD and control groups with 38 subjects each matched by sex, age, and the presence/absence of sleep bruxism. Four saliva samples were collected: upon waking, 30 min and 1 h after awakening (fasting), and at night (at 8 PM) on 2 alternate days to examine the diurnal profiles of cortisol and sAA. Anxiety symptoms were screened using the Multidimensional Anxiety Scale for Children (MASC-Brazilian version). Shapiro–Wilk test, Student’s t-test/Mann–Whitney U test, and correlation tests were used for data analysis. No significant differences were observed in the salivary cortisol area under the curve (AUCG mean ± SD = 90.22 ± 63.36 × 94.21 ± 63.13 µg/dL/min) and sAA AUCG (mean ± SD = 2544.52 ± 2142.00 × 2054.03 ± 1046.89 U/mL/min) between the TMD and control groups, respectively (p > 0.05); however, the clinical groups differed in social anxiety domain (t = 3.759; CI = 2.609, 8.496), separation/panic (t = 2.243; CI = 0.309, 5.217), physical symptoms (U = 433.500), and MASC total score (t = −3.527; CI = −23.062, −6.412), with a power of the test >80% and large effect size (d = 0.80), with no significant correlation between the MASC total score, cortisol, and sAA levels. Although children with TMD scored higher in anxiety symptoms, no difference was observed in the salivary stress biomarkers between children with and without TMD.