The aim of the current study was twofold: (1) to validate the internal structure of the general English (GE) section of the university entrance examination for Ph.D applicants into the English programs at state universities in Iran (Ph.D. UEE), and (2) to examine the factor structure invariance of the Ph.D. UEE across two proficiency levels. Structural equation modeling (SEM) was used to analyze the responses of a random sample of participants (N=1009) who took the test in 2014 to seek admission to English programs at Iranian state universities. First, four models (unitary, uncorrelated, correlated and higher-ordered) were estimated and compared to find the model that best represented the data. Then, the factor structure invariance of the test across two proficiency levels was explored using multigroup confirmatory factor analysis. The higher-order and correlated three-factor model showed the best fit to the data. The result also showed that the structure of the test remained invariant across both proficiency levels. These results supported the multi-componential view of language proficiency. It was found that there is no relationship between levels of language proficiency and the structure of the test. However, the results called into question the score-reporting policy for the PhD UEE and led to the conclusion that a single total score does not reflect the structure of the test.