Safe path planning is a crucial component in autonomous robotics. The many approaches to find a collision free path can be categorically divided into trajectory optimisers and sampling-based methods. When planning using occupancy maps, the sampling-based approach is the prevalent method. The main drawback of such techniques is that the reasoning about the expected cost of a plan is limited to the search heuristic used by each method. We introduce a novel planning method based on trajectory optimisation to plan safe and efficient paths in continuous occupancy maps. We extend the expressiveness of the state-of-the-art functional gradient optimisation methods by devising a stochastic gradient update rule to optimise a path represented as a Gaussian process. This approach avoids the need to commit to a specific resolution of the path representation, whether spatial or parametric. We utilise a continuous occupancy map representation in order to define our optimisation objective, which enables fast computation of occupancy gradients. We show that this approach is essential in order to ensure convergence to the optimal path, and present results and comparisons to other planning methods in both simulation and with real laser data. The experiments demonstrate the benefits of using this technique when planning for safe and efficient paths in continuous occupancy maps.