In Indonesia’s educational landscape, marked by historical struggles with low academic performance, the introduction of the Merdeka Curriculum presents a pivotal opportunity to integrate critical thinking skills into Islamic Religious education, empowering students to engage thoughtfully with religious teachings and promote pluralism and social cohesion. Critical thinking, as defined by scholars like Paul & Elder and Ennis, involves analyzing, evaluating, and synthesizing information systematically, and effective pedagogy is crucial for its cultivation. Given Indonesia’s diverse socio-cultural fabric, fostering critical thinking becomes paramount for encouraging mutual respect and understanding. However, a notable gap exists in research addressing the integration of critical thinking and pluralism within Islamic Religious Education in Indonesia. This study aims to investigate the development and implementation of critical thinking pedagogy within Islamic Religious Education, exploring the challenges of promoting pluralism within this context, particularly focusing on fourth-grade students in a private elementary school in Gresik, East Java. This qualitative study employs a descriptive case study design. The research examines factors influencing critical thinking pedagogy and highlights the teacher’s interactive methods, including storytelling and multicultural education. Challenges such as inadequate textbooks, varied prior knowledge among students, and limited teacher mindset are identified. Recommendations for future research include improving textbook comprehensiveness and assessing the impact of direct interactions on students’ perspectives.