Transient chaos is a ubiquitous phenomenon characterizing the dynamics of phase-space trajectories evolving towards a steady-state attractor in physical systems as diverse as fluids, chemical reactions, and condensed matter systems. Here we show that transient chaos also appears in the dynamics of certain efficient algorithms searching for solutions of constraint satisfaction problems that include scheduling, circuit design, routing, database problems, and even Sudoku. In particular, we present a study of the emergence of hardness in Boolean satisfiability (k-SAT), a canonical class of constraint satisfaction problems, by using an analog deterministic algorithm based on a system of ordinary differential equations. Problem hardness is defined through the escape rate κ, an invariant measure of transient chaos of the dynamical system corresponding to the analog algorithm, and it expresses the rate at which the trajectory approaches a solution. We show that for a given density of constraints and fixed number of Boolean variables N, the hardness of formulas in random k-SAT ensembles has a wide variation, approximable by a lognormal distribution. We also show that when increasing the density of constraints α, hardness appears through a second-order phase transition at α_{χ} in the random 3-SAT ensemble where dynamical trajectories become transiently chaotic. A similar behavior is found in 4-SAT as well, however, such a transition does not occur for 2-SAT. This behavior also implies a novel type of transient chaos in which the escape rate has an exponential-algebraic dependence on the critical parameter κ∼N^{B|α-α_{χ}|^{1-γ}} with 0<γ<1. We demonstrate that the transition is generated by the appearance of metastable basins in the solution space as the density of constraints α is increased.