Introduction: Stress-related disorders, including adjustment disorder and exhaustion disorder, are associated with cognitive complaints and prolonged sickness absence (SA). This study evaluated the effects of cognitive behavioral therapy (CBT) compared with an active control treatment (entitled General Health Promotion: GHP) on these outcomes and examined the association between cognitive impairment and SA. Methods: In this randomized clinical trial, 300 participants were randomized to CBT or GHP. SA data from the Swedish Social Insurance register were collected from 1 year before to 1 year after treatment. Cognitive functioning, assessed via a validated test battery, was measured at baseline, posttreatment, and 1-year follow-up (1YFU). Hurdle negative binomial models evaluated SA and linear mixed-effects models analyzed cognitive outcomes. Results: CBT and GHP had comparable effects on SA and cognitive functioning with no significant between-group effects (all p > 0.05). Analyzing effects across the entire sample, the number of SA days among those with any SA did not significantly change (p = 0.946) but the likelihood of having any SA decreased significantly by the 1YFU (OR = 0.92, 95% CI [0.87–0.96], p < 0.001). Independent of treatment group, overall cognitive functioning improved both posttreatment (d = −0.42, 95% CI [−0.6 to −0.25], p < 0.001) and at 1YFU (d = −0.72, 95% CI [−0.91 to −0.54], p < 0.001). Improvements in cognitive functioning pre- to posttreatment were associated with fewer SA days at the 1YFU (IRR = 0.54, 95% CI [0.33–0.87], p = 0.01). Conclusion: This study found no specific effect of CBT on SA or cognitive functioning for individuals with stress-related disorders. Cognitive functioning improved regardless of treatment. Early support before SA initiation is likely important to prevent long-term SA.