Dysphagia is a common concern. In an outpatient phoniatric and otorhinolaryngology clinic, approximately one fourth of dysphagia patients are classified as having non-organic, or functional dysphagia. This study aimed to evaluate symptom severity, health-related quality of life (HRQoL) and disability among dysphagia patients. Additionally, it focused on assessing the impact of flexible endoscopic evaluation of swallowing (FEES) and swallowing guidance particularly for patients with functional dysphagia. We recruited 60 consecutive dysphagia patients from our phoniatrics clinic. They completed the Eating Assessment Tool (EAT-10), the 15D Health-related Quality of Life Instrument and the World Health Organization Disability Assessment Schedule (WHODAS 2.0) questionnaires before their appointments. We performed FEES and gave swallowing guidance. One month later, the patients repeated the EAT-10, 15D, and WHODAS 2.0. At one-month follow-up, the EAT-10 scores of all 60 dysphagia patients (median age 65, range 18–89 years, 70% female), and the functional dysphagia patients (n = 15, 25%) had decreased significantly (p = 0.020, p = 0.029, respectively). Although the changes in the 15D and WHODAS 2.0 scores were insignificant, the score of WHODAS 2.0 item D3.3 concerning eating had decreased significantly in the functional dysphagia group (p = 0.020). Comparison of the whole dysphagia patient cohort to an age- and gender-standardized sample of the general population revealed significant differences in 15D total scores (p < 0.001) and 12 of the 15 dimensions. Dysphagia seems to significantly diminish patients’ HRQoL in comparison to that of the general population. A short FEES intervention with swallowing guidance may alleviate symptoms, especially in functional dysphagia.