Whether unconscious stimuli can modulate the preparation of a cognitive task is still controversial. Using a backward masking paradigm, we investigated whether the modulation could be observed even if the prime was made unconscious in 100% of the trials. In two behavioral experiments, subjects were instructed to initiate a phonological or semantic task on an upcoming word, following an explicit instruction and an unconscious prime. When the SOA between prime and instruction was sufficiently long (84ms), primes congruent with the task set instruction led to speedier responses than incongruent primes. In the other condition (36ms), no task set priming was observed. Repetition priming had the opposite tendency, suggesting the observed task set facilitation cannot be ascribed solely to perceptual repetition priming. Our results therefore confirm that unconscious information can modulate cognitive control for currently active task sets, providing sufficient time is available before the conscious decision.