Background <p>Studies on eating disorders (EDs) examining differences in the perception of family structures among patients with anorexia nervosa (AN) and bulimia nervosa (BN) are rare. In particular, intrafamilial differences in the assessment of family functioning and their potential therapeutical consequences remain underrepresented in current research.</p> Methods <p>Our sample comprised 540 patients diagnosed with ED and their parents, including 184 mothers and 156 fathers, who participated in the FamFINED study. Using the total score of the General Family Questionnaire (<i>Allgemeiner Familienbogen</i>; FBa), we compared the perceptions of family functioning among patients diagnosed with AN (<i>n</i> = 269) or BN (<i>n</i> = 271) including their respective parents.</p> Results <p>Among the study cohort, significant correlations were found between the total FBa scores of patients and their mothers (<i>n</i> = 180, <i>r</i> = 0.186, <i>p</i> = 0.012) as well as between patients and fathers (<i>n</i> = 155, <i>r</i> = 0.440, <i>p</i> &lt; 0.001). Furthermore, the total FBa score was significantly linked to the difference to the desired weight (<i>n</i> = 449, <i>r</i> = 0.174, <i>p</i> &lt; 0.001). Individuals with BN perceived greater family dysfunction, as indicated by a significantly higher total FBa score, compared to those with AN (59.37 ± 6.97 vs. 57.77 ± 8.28, <i>p</i> = 0.015). Similarly, mothers and fathers of AN patients reported lower total FBa scores than the parents in the BN group, but these differences did not reach statistical significance. Multiple linear regression analysis adjusted for patient age, body-mass index (BMI), presence of siblings, and highest educational attainment confirmed the significant association between the patient´s total FBa score and ED diagnosis (β = 1.92, 95%-confidence interval = 0.098–3.735, <i>p</i> = 0.039).</p> Conclusion <p>The study confirms that patients with BN perceive their families as significantly more dysfunctional compared to those with AN. In addition, our data indicate that, in families affected with ED, the difference between the desired and the actual weight significantly correlates with the total FBa score of the patients. Furthermore, we found that ED patients reporting higher total FBa scores also had parents who perceive their family structure as less functional.</p> <p><i>Clinical Trial registration</i>: ClinicalTrials.gov Identifier: NCT05339165.</p>