Some sensor systems are characterized by multiple simultaneous aperiodic emissions, with low signal-to-noise ratio and asynchronous detection. In these systems, complementary sets of sequences can be used to encode emissions, due to their suitable auto-correlation and cross-correlation properties. The transmission of a complementary set can be accomplished by interleaving the sequences of the set, generating a macro-sequence which is easily transmitted by a BPSK modulation. The detection of the macrosequence can be performed by means of efficient correlation algorithms with a notably decreased computational load and hardware complexity. This work presents a new hardware design in configurable logic of an efficient correlator for macrosequences generated from complementary sets of sequences. A generic implementation has been achieved, so the configuration can be changed according to the requirements of the application. The developed correlator has been tested in an ultrasonic pulse compression system in which real-time is needed. However, it is applicable in any multi-sensor or communication system where the goal is to make simultaneous emissions from different independent sources, minimizing mutual interference.