Speech fluency/disfluency can be evaluated by analyzing a range of phonetic and prosodic features. Deep neural networks are commonly trained to map fluency-related features into the human scores. However, the effectiveness of deep learning-based models is constrained by the limited amount of labeled training samples. To address this, we introduce a self-supervised learning (SSL) approach that takes into account phonetic and prosody awareness for fluency scoring. Specifically, we first pre-train the model using a reconstruction loss function, by masking phones and their durations jointly on a large amount of unlabeled speech and text prompts. We then fine-tune the pre-trained model using human-annotated scoring data. Our experimental results, conducted on datasets such as Speechocean762 and our non-native datasets, show that our proposed method outperforms the baseline systems in terms of Pearson correlation coefficients (PCC). Moreover, we also conduct an ablation study to better understand the contribution of phonetic and prosody factors during the pre-training stage.