In this paper, we tackle the Bayesian estimation of point process intensity as a function of covariates. We propose a novel augmentation of permanental process called augmented permanental process, a doubly-stochastic point process that uses a Gaussian process on covariate space to describe the Bayesian a priori uncertainty present in the square root of intensity, and derive a fast Bayesian estimation algorithm that scales linearly with data size without relying on either domain discretization or Markov Chain Monte Carlo computation. The proposed algorithm is based on a non-trivial finding that the representer theorem, one of the most desirable mathematical property for machine learning problems, holds for the augmented permanental process, which provides us with many significant computational advantages. We evaluate our algorithm on synthetic and real-world data, and show that it outperforms state-of-the-art methods in terms of predictive accuracy while being substantially faster than a conventional Bayesian method.