The purpose of this study was to know the learning difficulties experienced by third grade students of Mathematics Education Study Program during Project Based Learning (PjBL) implementation on Evaluation of Mathematics’ Learning Process and Result. This research used descriptive method with qualitative approach because it is relevant from the initial process to the final product, and research instrument used is in the form of interview sheet. The sample of this research is 68 third grade students of Mathematics Education Study Program of Faculty of Teaching and Educational Sciences, University of Swadaya Gunung Jati Cirebon. The study was conducted in the period of March - July 2016. Based on the results of this study it can be concluded that students' learning difficulties during the implementation of Project Based Learning caused by internal factors, that is lack of motivation, which can be seen from the lack of students in reading and looking for various references related to the material, they rely on one reference book only that used during lectures. This resulted to the lack of understanding in learning the Evaluation Instruments’ Quality which can be seen from the difficulty in classifying evaluation test questions based on Bloom's Taxonomy and arranging scoring guidelines, using validity formula, reliability, item discrimination, and index of difficulty to determine instrument quality, and difficulty in accomplishing the final product.