Scientific knowledge on depression and anxiety in patients with rare diseases during the COVID-19 pandemic is scarce; however, it is essential to perform comprehensive management of these patients. The aim of this study was to research how the situation caused by the SARS-CoV-2 pandemic has influenced the lives of patients with rare diseases regarding depression and anxiety. This Spanish study considered a heterogeneous population sample of 86 patients with confirmed diagnosis of different rare diseases. Participants took part in a cross-sectional online study by completing specific questionnaires on the study topic. Depression was measured using the Patient Health Questionnaire (PHQ-9), and the General Anxiety Disorder Scale (GAD-7) was used for evaluating anxiety. Data collection through an online questionnaire allowed for a greater population scope and therefore the inclusion patients of other nationalities in the study sample. Finally, as a general result, this study found that, in the face of the pandemic, anxiety and depression remained at a higher level in this group than in the general population, making these patients a vulnerable population group.