An apparatus and method for detecting a malicious domain cluster. The apparatus for detecting a malicious domain cluster includes a domain name server (DNS) data collection unit and a malicious domain cluster detection unit. The DNS data collection unit collects DNS traffic over a network, and stores the DNS traffic in a database. The malicious domain cluster detection unit generates a domain cluster based on the DNS data, learns the characteristics of normal and malicious clusters in the domain cluster, and detects whether the domain cluster is malicious based on the result of the learning.