This book consists of the lecture notes from the "Micro Scale Heat Transfer" course I have taught in the Mechanical Engineering program at the ITU Graduate School. The book addresses the problem of fluid flow and heat transfer in micro-scale channels. To achieve this, units of length ranging from the relatively small to the large, such as nanometers, micrometers, millimeters, kilometers, megameters, and gigameters are discussed first. Following this, fundamental theories are presented, and the mathematical modeling of fluid flow and heat transfer is formulated by considering various microchannel geometries across different phase states and flow regimes. Naturally, as in all engineering problems, solving the mathematical model is a necessity of analytical or numerical analysis in microchannels. In today's world, electrokinetic flow is highly topical, with application areas spanning from engineering to medicine. Taking this into consideration, the physics of electrokinetic flow is briefly discussed to an extent sufficient for an engineer, and the mathematical model is derived by providing two examples of microchannels related to electroosmotic flow. The prerequisite for reading this book is a knowledge of mathematics, thermodynamics, heat transfer, and fluid mechanics. Proceeding from this fact, the book was written for master's and doctoral students, and it directly concerns this audience. Undergraduate students can also comfortably read certain chapters of the book to expand their knowledge. Furthermore, it is a book that can benefit engineers working in industry, specifically in sectors such as cooling, household appliances, medical diagnostics, DNA scanning, chemistry, bio-measurement, separation, mixing, dispensing, and thermal cycling.