Provided are a memory controller determining degradation in endurance, a memory system including the memory controller, and a method of operating the memory controller. The memory controller includes: an error correction code (ECC) circuit configured to detect an error from data read from a memory device; and an endurance determination circuit configured to check a first counting value indicating a number of writing operations on the memory device and a second counting value indicating, based on the data read from the memory device, at least one of: a number of first memory cells of the memory device, each of the first memory cells having an error and a number of second memory cells of the memory device in a certain logic state, and configured to perform a first determination operation for determining whether endurance of the memory device has degraded based on a checking result.