Pronunciation assessment is a major challenge in the computer-aided pronunciation training system, especially at the word (phoneme)-level. To obtain word (phoneme)-level scores, current methods usually rely on aligning components to obtain acoustic features of each word (phoneme), which limits the performance of assessment to the accuracy of alignments. Therefore, to address this problem, we propose a simple yet effective method, namely Masked pre-training for Pronunciation Assessment (MPA). Specifically, by incorporating a mask-predict strategy, our MPA supports end-to-end training without leveraging any aligning components and can solve misalignment issues to a large extent during prediction. Furthermore, we design two evaluation strategies to enable our model to conduct assessments in both unsupervised and supervised settings. Experimental results on SpeechOcean762 dataset demonstrate that MPA could achieve better performance than previous methods, without any explicit alignment. In spite of this, MPA still has some limitations, such as requiring more inference time and reference text. They expect to be addressed in future work.