The suprachiasmatic nucleus (SCN) is the master clock of the brain. It is a network of neurons that behave like biological oscillators, capable of synchronizing and maintaining daily rhythms. The detailed structure of this network is still unknown, and the role that the connectivity pattern plays in the networks ability to generate robust oscillations has yet to be fully elucidated. In recent work, we used an information theory-based technique to infer the structure of the functional network for synchronization, from bioluminescence reporter data. Here, we propose a computational method to determine the directionality of the connections between the neurons. We find that most SCN neurons have a similar number of incoming connections, but the number of outgoing connections per neuron varies widely, with the most highly connected neurons residing preferentially in the core.