A method to perform unfolding with Gaussian processes (GPs) is presented. Using Bayesian regression, we define an estimator for the underlying truth distribution as the mode of the posterior. We show that in the case where the bin contents are distributed approximately according to a Gaussian, this estimator is equivalent to the mean function of a GP conditioned on the maximum likelihood estimator. Regularisation is introduced via the kernel function of the GP, which has a natural interpretation as the covariance of the underlying distribution. This novel approach allows for the regularisation to be informed by prior knowledge of the underlying distribution, and for it to be varied along the spectrum. In addition, the full statistical covariance matrix for the estimator is obtained as part of the result. The method is applied to two examples: a double-peaked bimodal distribution and a falling spectrum.