A DNA double-strand break (DSB) can be repaired accurately by homologous recombination. The Mre11-Rad50-Nbs1 (MRN) complex is responsible for initiating homologous recombination by degrading 5′-ended DNA strand, where its activation by the Ctp1 cofactor plays a pivotal role. Here, by using purified fission yeast proteins, we show that two major elements comprise MRN activation. First, phosphorylation of Ctp1 promotes the physical interaction between MRN and Ctp1. Second, the C terminus of Ctp1 activates nucleolytic processing of DSB ends. In the latter case, a small peptide comprising only 15 amino acids from the Ctp1 C terminus is sufficient to activate MRN. Our results elucidate the core elements underlying MRN activation by Ctp1.