Al/AlOx/Al tunnel junctions, also known as Josephson Junctions, are key components of many established and emerging electronic devices. They are an essential component of superconducting qubits. A major drawback is a lack of understanding of how the amorphous AlOx barrier influences the electron transport properties. In this work we combined Tight Binding Density Functional Theory (DFTB) with Non Equilibrium Greens Function (NEGF) to study computationally several Al/AlOx/Al with different barrier lengths. The simulations reveal a weak exponential relationship between barrier length and resistance of the device. However, considerable variability is found between junctions of similar barrier length. The calculations provide evidence of an “effective” barrier length significantly smaller than the actual (physical) barrier length. The resistance and effective barrier is found to be sensitively influenced by the local atomic structure of the amorphous barrier, which explains the junction to junction variability.