This study was designed to evaluate the association of COVID-19 quarantine with the mental health outcomes in the Kurdistan region of Iraq according to key measures of this study. We conducted a matched case-control study within the cohort of all quarantined persons from February 22 through March 31, 2020 (n=300) in Kurdistan region of Iraq. Participants were matched on gender, age, marital status, and education level. Mental health outcomes measured by General Health Questioner (GHQ-28), Impact of event scalerevised (IES-R), and Fear of COVID-19(FC-19S) using an online form. Data analyzed with a t-test and Multiple Regression analysis (confidence intervals=99%). The final study sample included 102 cases and 106 controls, (69% participation rate). Cases showed significantly higher scores in general health questionnaire(t=4.57, P<0.001) and its components (anxiety /insomnia, somatic syndrome, social dysfunction [P<0.001]), Post-traumatic symptoms (t=6.25, P<0.001), and Fear of COVID-2019 (t=3.04, P<0.001). The groups were not significantly different in the case of depression (t=1.95, P=0.06). Multivariable logistic regression analysis showed that after controlling for confounders (age, gender, education) mental health predicted with PTSD (OR,1;95%CI,0.45-0.78; P=.0001) and fear of COVID19(OR,0.55;95%CI,0.73-0.33; P=.0001). These findings suggest that quarantine significantly contributed to negative mental health outcomes in the Kurdistan region of Iraq where people are already affected by other stressors. These findings may inform decision and public health policy makers to prevent psychological complications while designing and applying measures in the face of other major public health emergencies.