We investigate theoretically the noise and the full counting statistics of electrons that are emitted from a superconductor into two spatially separated quantum dots by the splitting of Cooper pairs and further on collected in two normal-state electrodes. With negatively biased drain electrodes and a large superconducting gap, the dynamics of the Cooper pair splitter can be described by a Markovian quantum master equation. Using techniques from full counting statistics, we evaluate the electrical currents, their noise power spectra, and the power-power correlations in the output leads. The current fluctuations can be attributed to the competition between Cooper pair splitting and elastic cotunneling between the quantum dots via the superconductor. In one regime, these processes can be clearly distinguished in the cross-correlation spectrum with peaks and dips appearing at characteristic frequencies associated with elastic cotunneling and Cooper pair splitting, respectively. We corroborate this interpretation by analyzing the charge transport fluctuations in the time domain, specifically by investigating the g((2)) function of the output currents. Our work identifies several experimental signatures of the fundamental transport processes involved in Cooper pair splitting and provides specific means to quantify their relative strengths. As such, our results may help guide and interpret future experiments on current fluctuations in Cooper pair splitters.