Teaching Science innovatively has become a key motivation in educational parlance to uplift the academic achievement of the learners. There are numerous teaching strategies and skills developed by educationists, researchers and teachers to teach the subject creatively in the classroom. Thinking Maps is one such teaching strategy that enables the learner to make their thought processes visible during the learning processes. Although there are several studies indicating the positive impacts of using Thinking Maps as a teaching-learning strategy, there is no established study conducted in the Bhutanese context to investigate its effectiveness. The study on learners' perception and academic achievement on the use of Thinking Maps as a learning strategy in class nine chemistry was aimed to investigate the effectiveness of using Thinking Maps as a teaching strategy in Damphu Middle Secondary School (DMSS). The pre-test and post-test were administered for both control and experimental groups to examine the performance level in chemistry before and after the intervention. Similarly, five-pointed Likert-type item survey questionnaires were administered for the experimental group to examine the influence of learners' perceptions. In addition, anecdotal records were maintained throughout the treatment for qualitative information. Results were analysed using descriptive and inferential statistics. Document analysis was done for the anecdotal records. While pre-test and post-test showed a change in mean test scores, rating scores from survey questionnaires indicated a positive impression towards Thinking Maps as a learning strategy. The overall findings indicated that the use of Thinking Maps as a teaching-learning strategy improves learners' achievement scores. It is recommended that teachers incorporate Thinking Maps as an alternative strategy into their lesson delivery.