The aim of our study was to assess the relationship between the concentration/activity of salivary stress biomarkers (cortisol, α-amylase) and the psychological profile of patients with oral lichen planus (OLP) and primary burning mouth syndrome (BMS). A total of 160 subjects participated in this case–control study: 60 patients with OLP; 60 patients with primary BMS; and 40 control subjects. Unstimulated whole saliva (UWS) was collected between 9 and 10 a.m. Salivary biomarkers were analyzed by enzyme-linked immunosorbent assays (ELISAs). Psychological assessment was evaluated with the Depression, Anxiety, and Stress Scale (DASS-21). The patients with primary BMS had higher salivary cortisol concentrations and α-amylase activity (0.52 vs. 0.44 µg/dL; 160,531 vs. 145,804 U/L; one-way analysis of variance (ANOVA) with post hoc Scheffe test) compared with patients with OLP. The patients with primary BMS had statistically significant higher scores for depression, anxiety, and stress compared with patients with OLP and control subjects (p < 0.001, Kruskal–Wallis test). There was a strong positive correlation between anxiety and depression, stress and depression, and stress and anxiety in patients with OLP and BMS (p < 0.001 and p < 0.001, respectively; Spearman’s correlation). There was a good positive correlation between symptom intensity (pain/burning) and psychological profile (depression, anxiety, stress) in patients with primary BMS (r = 0.373, p = 0.003; r = 0.515, p < 0.001; r = 0.365, p = 0.004, respectively; Spearman’s correlation). This case–control study is the first to compare the psychoendocrinological profile of patients with two different oral diseases. The patients with BMS showed a higher concentration/activity of salivary stress biomarkers (cortisol, α-amylase) and a stronger association with mental disorders compared with patients with OLP. However, an interdisciplinary psychoneuroimmunological approach is equally important in both patient groups (OLP and BMS), regardless of whether mental disorders are the cause or the consequence.