Eating disorders are a global burden and present personal, family, and societal costs. Most evidence in the literature is based on the relationship between a poor family environment and eating disorders, and the evidence of gender interaction in eating disorders is inconsistent. This study aimed to investigate the relationship between family functioning and disordered eating patterns, the mediating role of negative automatic thoughts, and the moderating role of gender. A sample of 440 (70.9% females, aged 18–21) participated in this study. They completed the Eating Attitudes Test (EAT-26), the Automatic Thoughts Questionnaire (ATQ negative), and the Brief Family Relationship Scale (BFRS). PROCESS MACRO was used to study these relationships. The main findings revealed that family functioning was negatively associated with eating disorders, and that this relationship was negatively mediated by automatic thoughts. Moreover, gender moderated those relationships, and more intensely in females. The results of this study postulate that the prevention of eating disorders should be directed at training individuals to challenge negative thoughts and encourage healthy individuals to be gender mindful.