We present **JPharmatron**, a Japanese domain-specific large language model (LLM) for the pharmaceutical field, developed through continual pre-training on two billion Japanese pharmaceutical tokens and eight billion English biomedical tokens. For rigorous evaluation, we introduce **JPharmaBench**, a benchmark suite consisting of three new benchmarks: YakugakuQA, based on national pharmacist licensing exams; NayoseQA, which tests cross-lingual synonym and terminology normalization; and SogoCheck, a novel task involving cross-document consistency checking.We evaluate our model against open-source medical LLMs and commercial models, including GPT-4o. Experimental results show that **JPharmatron** outperforms existing open models and achieves competitive performance with commercial ones.Interestingly, even GPT-4o performs poorly on SogoCheck, suggesting that cross-sentence consistency reasoning remains an open challenge.**JPharmatron** enables secure and local model deployment for pharmaceutical tasks, where privacy and legal constraints limit the use of closed models. Besides, **JPharmaBench** offers a reproducible framework for evaluating Japanese pharmaceutical natural language processing. Together, they demonstrate the feasibility of practical and cost-efficient language models for Japanese healthcare and pharmaceutical sectors.Our model, codes, and datasets are available on HuggingFace: https://huggingface.co/collections/EQUES/jpharmatron and https://huggingface.co/collections/EQUES/jpharmabench.