Abstract Background The COVID‐19 pandemic has spread across the world, leading to government measures associated with a negative impact on mental health. The aim of this study was to evaluate the impact of the pandemic on depression, anxiety and resilience in Dutch people with cystic fibrosis (PwCF) or primary ciliary dyskinesia (PwPCD) and their caregivers. Methods Adolescents (12–17 years) and caregivers of children (0–17 years) with CF, and adolescents, adults and caregivers of children with PCD completed questionnaires on depression, anxiety and resilience between September 2020 and February 2021. The psychosocial impact of COVID‐19 was measured by the Exposure and Family Impact Survey (CEFIS) Part 2. Mixed model analyses compared depression and anxiety results to participants' prepandemic scores. Results One hundred ten participants (10 PwCF, 31 PwPCD, 52 CF caregivers, 17 PCD caregivers) completed questionnaires during the pandemic. Prepandemic outcomes were available for 87 participants. The prevalence of symptoms of depression and anxiety (PHQ‐9 or GAD‐7 scores ≥5) in PwCF and PwPCD and their caregivers before and during the pandemic was high, with an increase in depression in PwCF (2.75; 95% confidence interval: 0.82–4.68) and increase in anxiety in CF caregivers (1.03; 0.09–1.96) during the pandemic. Resilience was within the normal range for all groups, CEFIS scores corresponded to a low to normal impact. Conclusion PwCF and PwPCD and their caregivers were at risk of elevated depression and anxiety symptoms both before and during the pandemic, which emphasizes the importance of mental health screening and psychological care in CF and PCD.