We study the finite temperature phase diagram of the Heisenberg-Kitaev model on a three dimensional hyperhoneycomb lattice. Using semiclassical analysis and classical Monte-Carlo simulations, we investigate quantum and thermal order-by-disorder, as well as the magnetic ordering temperature. We find the parameter regime where quantum and thermal fluctuations favor different magnetic orders, which leads to an additional finite temperature phase transition within the ordered phase. This transition, however, occurs at a relatively low temperature and the entropic effects may dominate most of the finite temperature region below the ordering temperature. In addition, we explore the magnetization process in the presence of a magnetic field and discover spin-flop transitions which are sensitive to the applied-field direction. We discuss implications of our results for future experiments on a hyperhoneycomb lattice system such as the recently discovered β-Li2IrO3.