Endurance and ultra-endurance running impose substantial physical and psychological demands, leading athletes to experience intense emotional states before, during, and after competitions. Accordingly, there is a paucity of evidence comparing mood profiles between endurance and ultra-endurance runners competing in trail and mountain events. The aim of this study was to characterize the mood profile of endurance and ultra-endurance runners participating in La Misión Brasil 2024 and to analyze its relationship with sleep quality. This prospective cross-sectional study included 193 runners, divided into an endurance group (n = 118; men = 75; women = 43) and an ultra-endurance group (n = 75; men = 60; women = 15), who participated in the same competition according to the proposed distances. La Misión Brasil is a trail running event with race distances ranging from 25 to 80 km and substantial elevation gain. One week prior to the competition, participants completed questionnaires assessing mood state, anxiety, psychological health, and sleep quality. Comparisons between groups (endurance group vs. ultra-endurance group) and sexes were performed using independent t-tests, Mann–Whitney tests, and generalized linear models, whereas associations were examined using Spearman’s correlation. The results indicated higher vigor levels in the ultra-endurance group (p = 0.020) and greater overall fatigue in the endurance group (p = 0.027). Regarding sex differences, men exhibited higher vigor (p = 0.004), whereas women presented higher total mood disturbance and anxiety scores (trait anxiety and state anxiety; p < 0.05). Correlational analyses revealed that poorer sleep quality scores were moderately associated with higher total mood disturbance (r2 = 0.45) and anxiety levels (trait anxiety: r2 = 0.47; state anxiety: r2 = 0.48). Additionally, strong correlations were observed between negative mood states, total mood disturbance, and anxiety (r2 > 0.50). Overall, endurance and ultra-endurance runners demonstrated a favorable mood profile; however, the psychological demands of these modalities are associated with relevant interactions between sleep, mood, and anxiety.