Self-injurious thoughts and behavior (SITB), including passive and active suicidal ideation (SI) and self-harm (SH) urges and behavior, are critical phenomena to predict and target during treatment. Partial hospital programs (PHP) provide unique opportunities to understand how negative affect (e.g., depression and anger) and SITB fluctuate daily. The current study aimed to explore associations between aspects of negative affect (depression and anger) and types of SITB throughout PHP treatment. PHP patients (N = 1625) who attend at least five days of treatment were included in the current sample. Anger-related symptoms, depressive symptoms, SH urges, SH occurrence, passive SI, and active SI were measured daily. A series of generalized linear mixed models were conducted to examine whether depressive and anger-related symptoms predicted SITB across patients (between-person) and throughout PHP treatment (within-person). At the between-person level, higher average depressive symptoms predicted greater severity of all forms of SITB, whereas higher average anger-related symptoms predicted greater severity SH urges and occurrence. At the within-person level, increases in depressive symptoms were associated with increases in all aspects of SITB, whereas increases in anger-related symptoms predicted increases in passive and active SI. The current study suggests that monitoring changes in negative affect throughout treatment can provide possible targets to reduce SITB.