This paper presents GPFC, a novel Graphics Processing Unit (GPU) Phase Folding and Convolutional Neural Network (CNN) system to detect exoplanets using the transit method. We devise a fast folding algorithm parallelized on a GPU to amplify low signal-to-noise ratio transit signals, allowing a search at high precision and speed. A CNN trained on two million synthetic light curves reports a score indicating the likelihood of a planetary signal at each period. GPFC improves on speed by three orders of magnitude over the predominant Box-fitting Least Squares (BLS) method. Our simulation results show GPFC achieves 97% training accuracy, higher true positive rate at the same false positive rate of detection, and higher precision at the same recall rate when compared to BLS. GPFC recovers 100% of known ultra-short-period planets in Kepler light curves from a blind search. These results highlight the promise of GPFC as an alternative approach to the traditional BLS algorithm for finding new transiting exoplanets in data taken with Kepler and other space transit missions such as K2, TESS and future PLATO and Earth 2.0.