This disclosure describes techniques for handling divergent thread conditions in a multi-threaded processing system. In some examples, a control flow unit may obtain a control flow instruction identified by a program counter value stored in a program counter register. The control flow instruction may include a target value indicative of a target program counter value for the control flow instruction. The control flow unit may select one of the target program counter value and a minimum resume counter value as a value to load into the program counter register. The minimum resume counter value may be indicative of a smallest resume counter value from a set of one or more resume counter values associated with one or more inactive threads. Each of the one or more resume counter values may be indicative of a program counter value at which a respective inactive thread should be activated.