This article is based on the knowledge that complex thinking as a construct is nowadays shaping a system of meta-competencies which depends entirely on synergy at all its levels. In higher education contexts, it is well known that the development of transversal competencies allows fostering a better recognition and adaptation to the environment. However, the indistinct use of some concepts that allude to competencies generates confusion regarding what they imply, both theoretically and practically. Consequently, the present article analyzes the differences between complex thought and complex thinking, as relevant concepts, and competencies in higher education. We analyzed to what extent the concept of complex thought is a possible starting point for the adoption of the term and development of the competence of complex thinking, and how this is permeating all branches of knowledge. A qualitative research methodology was used to support the present theoretical reflection, through a critical reflection of the literature. Both concepts, their uses, and implications were analyzed through a compilation of scientific papers, which allowed an entire observation, and document analysis to ensure objective study. The present work presents practical implications in higher education contexts: 1) complex thought has become a relevant matter for explaining the multidisciplinary from theory of knowledge in epistemology, and 2) complex thinking has become a mean for ensuring new academic skills and strengths for problem solving among students in higher education.