An in-depth knowledge of pedagogical approaches can help improve the formulation of effective and efficient pedagogy, tools and technology to support and enhance the teaching and learning of Mathematics in higher institutions. This study investigated students' perceptions of the challenges of blended e-learning tools in the teaching and learning of mathematics. The study is a descriptive survey design conducted with thirty undergraduate students of the University of Uyo, Nigeria. A research questionnaire of students' perceptions on the challenges of blended e-learning tools in mathematics was used to elicit responses. The questionnaire has three sections of the perceived challenges of blended e-learning tools in mathematics; availability, accessibility and students' ICT skills towards utilization of blended e-learning tools. Data were analyzed using SPSS at the 0.05 level of significance. The results revealed non-availability, non-accessibility and inadequate students' ICT skills towards the utilization of blended e-learning tools for the teaching and learning mathematics. The overall results revealed that there is significant difference on students' perceptions towards the challenges of blended e-learning tools. Based on the research findings, the institution and instructors need to identify the perceived challenges and opportunities of blended e-learning and provide practical support such as provision of Virtual Learning Environment (VLE) to diversified students learning of mathematics. The study could be used as proactive response towards the institutions' preparedness on the development of blended e-learning approaches in terms of content design models and pedagogical approach for the teaching and learning of mathematics.