A system for treating mononuclear cells for an extracorporeal photopheresis procedure, comprising: a fluid circuit comprising a chamber, a priming fluid container, and an irradiation container; a separator configured to work in association with the fluid circuit to rotate the chamber about a rotational axis and convey whole blood into an inlet region of the chamber for separation into a red blood cell component, a plasma component, and the mononuclear cell component; and a microprocessor-based controller in communication with the separator, wherein the controller is configured to: prime the fluid circuit with priming fluid from the priming fluid container; direct whole blood derived from a blood source into the fluid circuit; separate within the separator the whole blood into the red blood cell component, the mononuclear cell component, and the plasma component; return a first portion of the red blood cell component and a first portion of the plasma component to the blood source; add a photoactivation agent to the mononuclear cell component to create an agent-added mononuclear cell component; irradiate the agent-added mononuclear cell component in the irradiation container to create a photoactivated mononuclear cell component; and incubate for a period of time at least a portion of the photoactivated mononuclear cell component to create an incubated photoactivated mononuclear cell component. a fluid circuit comprising a chamber, a priming fluid container, and an irradiation container; a separator configured to work in association with the fluid circuit to rotate the chamber about a rotational axis and convey whole blood into an inlet region of the chamber for separation into a red blood cell component, a plasma component, and the mononuclear cell component; and a microprocessor-based controller in communication with the separator, wherein the controller is configured to: prime the fluid circuit with priming fluid from the priming fluid container; direct whole blood derived from a blood source into the fluid circuit; separate within the separator the whole blood into the red blood cell component, the mononuclear cell component, and the plasma component; return a first portion of the red blood cell component and a first portion of the plasma component to the blood source; add a photoactivation agent to the mononuclear cell component to create an agent-added mononuclear cell component; irradiate the agent-added mononuclear cell component in the irradiation container to create a photoactivated mononuclear cell component; and incubate for a period of time at least a portion of the photoactivated mononuclear cell component to create an incubated photoactivated mononuclear cell component. prime the fluid circuit with priming fluid from the priming fluid container; direct whole blood derived from a blood source into the fluid circuit; separate within the separator the whole blood into the red blood cell component, the mononuclear cell component, and the plasma component; return a first portion of the red blood cell component and a first portion of the plasma component to the blood source; add a photoactivation agent to the mononuclear cell component to create an agent-added mononuclear cell component; irradiate the agent-added mononuclear cell component in the irradiation container to create a photoactivated mononuclear cell component; and incubate for a period of time at least a portion of the photoactivated mononuclear cell component to create an incubated photoactivated mononuclear cell component.