In this paper, we propose a new Transformer neural machine translation (NMT) model that incorporates dependency relations into self-attention on both source and target sides, dependency-based self-attention. The dependency-based self-attention is trained to attend to the modifiee for each token under constraints based on the dependency relations, inspired by Linguistically-Informed Self-Attention (LISA). While LISA is originally proposed for Transformer encoder for semantic role labeling, this paper extends LISA to Transformer NMT by masking future information on words in the decoder-side dependency-based self-attention. Additionally, our dependency-based self-attention operates at sub-word units created by byte pair encoding. The experiments show that our model improves 1.0 BLEU points over the baseline model on the WAT’18 Asian Scientific Paper Excerpt Corpus Japanese-to-English translation task.