The present disclosure pertains to waking a subject from a period of wakeful sleep by modulation of a flow of breathable gas being delivered to the airway of the subject, with the modulation being performed based on a monitoring of wakefulness of the subject during sleep Typical sleep cycles comprise periods of deeper sleep and/or periods or lighter (wakeful) sleep. Waking during lighter stages of sleep may result in feeling more energetic and well-rested compared to waking from deeper sleep. Sleep therapy such as, for example, continuous positive airway pressure (CPAP), typically monitors sleep characteristics of a subject. These sleep characteristics comprise one or more of tidal volume, pressurized gas leakage (indicating movement), respiration rate, and/or other characteristics. During use of sleep therapy devices, sleep characteristics may be collected during therapy that can be used to determine whether the patient is in light sleep or deep sleep. The present disclosure contemplates utilizing a sleep therapy device in combination with the system described herein to collect sleep characteristics of a subject during sleep, and to wake the subject from wakeful sleep during an alarm window so the subject may feel as well rested and energetic as possible.