BackgroundTobacco control should be a higher public health priority in Japan. Some workplaces provide smoking cessation support and connect employees to effective smoking cessation treatments such as outpatient clinics. However, tobacco control measures have not been sufficiently implemented in Japan, especially in small- and medium-sized enterprises (SMEs), where resources are limited. Organizational commitment and consistent leadership are crucial to facilitate implementation, but research on whether supporting organizational leaders leads to health behavior changes among employees is limited.MethodsThis hybrid type II cluster randomized effectiveness implementation trial (eSMART-TC) aims to examine the effects of interactive assistance for SME management on health and implementation outcomes. We will provide interactive assistance to employers and health managers for 6 months, aiming to promote the utilization of reimbursed smoking cessation treatments by public health insurance and to implement smoke-free workplaces. The intervention will consist of three strategies: supporting employees through campaigns, tailored ongoing facilitation, and ensuring executive engagement and support. The primary health and implementation outcomes will be salivary cotinine-validated 7-day point-prevalence abstinence rate, and the adoption of two recommended measures (promoting utilization of smoking cessation treatment and implementing smoke-free workplaces) 6 months after the initial session, respectively. Other outcomes for implementation (e.g., penetration of smoking cessation clinic visits), health (e.g., salivary cotinine-validated 7-day point-prevalence abstinence rate at 12 months), and process (e.g., adherence and potential moderating factors) will be collected via questionnaires, interviews, logbooks, and interventionists’ notes at 6 and 12 months. An economic analysis will be undertaken to assess the cost-effectiveness of the implementation interventions at 12 months.DiscussionThis will be the first cluster randomized controlled trial to evaluate the effectiveness of an implementation intervention with interactive assistance for employers and health managers in SMEs on smoking cessation and implementation of evidence-based tobacco control measures in SMEs. The findings of this trial targeting management in SMEs have the potential to accelerate the implementation of evidence-based smoking cessation methods as well as abstinence rates among employees in SMEs across Japan.Trial registrationThe study protocol has been registered in the UMIN Clinical Trials Registry (UMIN-CTR; ID: UMIN000044526). Registered on 06/14/2021.Supplementary InformationThe online version contains supplementary material available at 10.1186/s43058-023-00444-0.