The objective of this study is to compare treatment trajectories in anorexia nervosa (AN) and atypical AN. Adolescents and adults with AN (n = 319) or atypical AN (n = 67) in a partial hospitalization program (PHP) completed diagnostic interviews and self-report questionnaires measuring eating disorder (ED), depression, and anxiety symptoms throughout treatment. Premorbid weight loss did not differ between diagnoses. Individuals with atypical AN had more comorbid diagnoses, but groups did not differ on specific diagnoses. ED psychopathology and comorbid symptoms of depression/anxiety did not differ at admission between groups nor did rate of change in ED psychopathology and comorbid symptoms of depression/anxiety from admission to 1-month. From admission to discharge, individuals with atypical AN had a faster reduction in ED psychopathology and comorbid symptoms of depression and anxiety (ps < 0.05; rs = 0.01-0.32); however, there were no group differences in ED psychopathology or depression symptoms at discharge (ps>.50; ds = .01-.30). Individuals with atypical AN had lower anxiety at discharge compared to individuals with AN (p = 0.05; d = .4). Length of stay did not differ between groups (p = 0.11; d = .21). Groups had similar ED treatment trajectories, suggesting more similarities than differences. PHP may also be effective for AAN. This study supports previous research that individuals with AN and atypical AN have more similarities than differences. Results from this study indicate that individuals with AN and atypical AN have similar treatment outcomes for both ED psychopathology and depressive symptoms; however, individuals with atypical AN have lower anxiety symptoms at discharge compared to individuals with AN. AN and atypical AN also have more symptom similarity at admission and throughout treatment, which challenges their current designation as distinct disorders.