This article proposes a novel visual framework for detecting tunnel crossings/junctions in underground mine areas towards the autonomous navigation of Micro Aeril Vehicles (MAVs). Usually mine environments have complex geometries, including multiple crossings with different tunnels that challenge the autonomous planning of aerial robots. Towards the envisioned scenario of autonomous or semi-autonomous deployment of MAVs with limited Line-of-Sight in subterranean environments, the proposed module acknowledges the existence of junctions by providing crucial information to the autonomy and planning layers of the aerial vehicle. The capability for a junction detection is necessary in the majority of mission scenarios, including unknown area exploration, known area inspection and robot homing missions. The proposed novel method has the ability to feed the image stream from the vehicles’ on-board forward facing camera in a Convolutional Neural Network (CNN) classification architecture, expressed in four categories: 1) left junction, 2) right junction, 3) left & right junction, and 4) no junction in the local vicinity of the vehicle. The core contribution stems for the incorporation of AlexNet in a transfer learning scheme for detecting multiple branches in a subterranean environment. The validity of the proposed method has been validated through multiple data-sets collected from real underground environments, demonstrating the performance and merits of the proposed module.