In this work, we investigated a platform for real-time emulsion droplet detection and size measurement in optofluidic platforms. An 8.2 µm core diameter input optical fiber and a multi-mode Gradient Refractive Index (GRIN) output fiber were integrated into an acrylic microfluidic channel platform consisting of three layers. Water-in-oil emulsions were investigated, since relevant applications have emerged in the recent past for these types of emulsions, such as drug encapsulation as well as droplet-based Polymerase Chain Reaction (PCR) amplification of DNA, among others. The main contribution of this work is in understanding the main physical phenomena (i.e., total internal reflection, refraction, and interference) behind the complex transmittance pattern obtained for these droplets. For this purpose, a frequency domain electromagnetic wave propagation modelling of the structure using the Finite Element Method (FEM) was used along with experimental measurements.