There are provided a controller, an electronic system including the same, and an operating method of the controller and the memory system. The controller includes: a randomizing circuit configured to generate random data having a set number of bits; a masking circuit configured to output select random data by extracting some data according to a number of bits on which a partial encoding operation is to be performed, among the random data; an operating circuit configured to output encoded data and a portion of original data, by performing an operation sequentially on the original data and the select random data; and a cyclic redundancy check circuit configured to generate a cyclic redundancy check value by performing a cyclic redundancy check on the encoded data and the portion of original data, and output partially encoded data including the cyclic redundancy check value, the portion of original data, and the encoded data.