Reasoning large language models (LLMs) have recently made much progress in complex problem-solving, leveraging internal reasoning (or thought) to guide their solution generation. However, existing LLM-based counseling agents, including those using Motivational Interviewing (MI), generate responses without explicitly aligning thoughts with counseling techniques, limiting their effectiveness. We propose MIThinker, a lightweight thinking model that generates therapeutic thoughts to guide MI counseling agents in strategy selection and response generation. To overcome the lack of annotated thought data, we introduce AugR1-MI, an automated pipeline that reverse-engineers counselor’s thoughts from observed responses. Through two-stage training combining supervised fine-tuning and reinforcement learning, MIThinker demonstrates improved theory-of-mind assessment and strategy alignment. Comprehensive evaluations show that MindfulMI, our agent leveraging MIThinker, achieves MI competency comparable to state-of-the-art systems with an order of magnitude less computation.