<p>Strengthening the capacities of individuals to identify implementation challenges and enact strategies to overcome them is vital and can be achieved through implementation research. However, training in implementation research is not readily available and accessible to researchers and public health practitioners in East Africa. Two research institutions implemented a short course training in implementation research. Kirkpatrick’s model and Cooke’s framework were employed to evaluate the impact of this course. We found that participants were very satisfied with the training, with 98% of them agreeing or agreeing strongly that facilitators displayed mastery of content and that they intend to apply what they learned at work. What they liked the most about the training was its interactive and participatory nature. There was a statistically significant increase in knowledge and skills (<i>p</i> &lt; 0.05) post-training. The focus group discussions revealed that the training contributed to the development of participants’ confidence in conducting implementation research. However, participants suggested allocating more time to improve the training. Followup assessment at least one year and nine months post-training showed that participants applied acquired knowledge and skills at work and their institutions benefitted. To our knowledge, this is the first study in which a mixed methods approach in combination with Kirkpatrick’s model and Cooke’s framework are employed to evaluate the impact of a short course training in implementation research. In future offerings of this course, consideration should be made to extending course duration to over one week, using 360-degree assessment to capture diverse perspectives, and addressing identified implementation challenges.</p>