Research on transcranial magnetic stimulation (TMS) combined with encephalography feedback (EEG-TMS) has shown that the phase of the sensorimotor mu rhythm is predictive of corticospinal excitability. Thus, if the subject-specific optimal phase is known, stimulation can be timed to be more efficient. In this paper, we present a closed-loop algorithm to determine the optimal phase linked to the highest excitability with few trials. We used Bayesian optimization as an automated, online search tool in an EEG-TMS simulation experiment. From a sample of 38 participants, we selected all participants with a significant single-subject phase effect (N = 5) for simulation. We then simulated 1000 experimental sessions per participant where we used Bayesian optimization to find the optimal phase. We tested two objective functions: Fitting a sinusoid in Bayesian linear regression or Gaussian Process (GP) regression. We additionally tested adaptive sampling using a knowledge gradient as the acquisition function compared with random sampling. We evaluated the algorithm's performance in a fast optimization (100 trials) and a long-term optimization (1000 trials). For fast optimization, the Bayesian linear regression in combination with adaptive sampling gives the best results with a mean phase location accuracy of 79 % after 100 trials. With either sampling approach, Bayesian linear regression performs better than GP regression in the fast optimization. In the long-term optimization, Bayesian regression with random sampling shows the best trajectory, with a rather steep improvement and good final performance of 87 % mean phase location accuracy. We show the suitability of closed-loop Bayesian optimization for phase selection. We could increase the speed and accuracy by using prior knowledge about the expected function shape compared with traditional Bayesian optimization with GP regression.