The advent of generative AI (GenAI) tools in higher education challenges fundamental assumptions about academic authorship, students’ cognitive development and how writing cultivates critical thinking (CT). This systematic mapping study synthesized emerging research on how GenAI is reshaping the relationship between academic writing and CT in higher education. Drawing on 25 peer-reviewed studies published between 2023 and 2025, we analyzed conceptualizations of CT and academic writing, identified pedagogical approaches, and examined the use of GenAI tools across a range of disciplines, educational levels, and geographic contexts. Findings revealed that interest in the use of GenAI in academic writing is global and spans all disciplines and higher educational levels. However, only a minority of studies drew on robust theoretical frameworks. CT was conceptualized predominantly within a cognitive skills paradigm, while broader understandings linked to criticality and critical pedagogy were largely absent. Pedagogical models were rare and mostly untested, and educators’ perspectives were underrepresented. While GenAI was seen as supporting writing processes, its potential to foster or hinder CT remained contested. Future research should broaden conceptual foundations, include educator perspectives, and prioritize pedagogical design and evaluation. Rethinking academic writing as a transformative practice may require moving beyond the cognitive paradigm towards more participatory and ethically grounded approaches to CT.