Although EFL learners pass different courses in writing at university and are expected to be able to express their thoughts in various forms of writing, their texts suffer from many problems. Therefore, the current study aimed to identify the type of problems that postgraduate EFL learners encounter in writing their thesis proposals. To this end, first, the problems marked by supervisors in thirty-two proposals written by TEFL and Translation Studies students were classified into two general categories: macro and micro problems. Then, these problems were classified based on Halliday and Hassan’s (1976) and Tardy’s (2009) models of academic genre. After that, a questionnaire about writing problems was administered to participants to elicit their perceptions towards writing MA proposals. The responses were then analyzed according to Dornyei’s (2003) suggestions for analyzing qualitative data. The findings revealed that discoursal and linguistic problems were among the highest frequent problems. The analysis of the questionnaires also indicated that EFL postgraduate learners hold negative attitude towards proposal writing, and considered discoursal problems as their major challenge in writing. There was consistency between their ideas and the real problems.