Fear of COVID-19 can have adverse mental health consequences in vulnerable patients with pre-existing conditions. We aimed to validate The COVID-19 Fears Questionnaire for Chronic Medical Conditions in Lithuania and to evaluate fears of COVID-19 in patients with pre-existing conditions. Between October and December, 2020, 371 respondents with pre-existing conditions completed an online survey including the 10-item COVID-19 Fears Questionnaire for Chronic Medical Conditions (COVID-19 fears), Patient Health Questionnaire-8 (PHQ-8; depressive symptoms), Generalised Anxiety Disorders-7 (GAD-7; anxiety symptoms) and Impact of Events Scale Revised (IES-R; posttraumatic stress symptoms). The majority of participants were women (84%) and from 41 to 60 years old (46%). The most common pre-existing conditions were respiratory diseases (33%) and diabetes (22%). Mean total score on the COVID-19 Fears Questionnaire was 24.89 ± 8.79. Exploratory factor analysis yielded one-factor solution with the Cronbach’s coefficient alpha of 0.913. The highest rated COVID-19 fears were infection of close people, inability to receive treatment for COVID-19 and pre-existing condition and fear of severe complications because of the pre-existing condition. There was moderate to strong correlation of the 10-item COVID-19 Fears Questionnaire for Chronic Medical Conditions score with scores on the PHQ-8 (r = 0.371), GAD-7 (r = 0.358) and IES-R (r = 0.553; all p < 0.001). Test-retest reliability was adequate. The 10-item COVID-19 Fears Questionnaire for Chronic Medical Conditions has good psychometric properties in patients with pre-existing conditions and greater fear is associated with worse mental health. Consideration of COVID-19 fears is important for optimised care of patients with pre-existing during the pandemic.