Bayesian models often involve a small set of hyperparameters determined by maximizing the marginal likelihood. Bayesian optimization is an iterative method where a Gaussian process posterior of the underlying function is sequentially updated by new function evaluations. We propose a novel Bayesian optimization framework for situations where the user controls the computational effort and therefore the precision of the function evaluations. This is a common in econometrics where the marginal likelihood is often computed by Markov chain Monte Carlo or importance sampling methods. The new acquisition strategy gives the optimizer the option to explore the function with cheap noisy evaluations and therefore find the optimum faster. The method is applied to estimating the prior hyperparameters in two popular models on US macroeconomic time series data: the steady-state Bayesian vector autoregressive (BVAR) and the time-varying parameter BVAR with stochastic volatility.