Planarian regeneration involves a complex series of cellular events, precisely choreographed in space and time. Time-lapse imaging can provide powerful insights into tissue dynamics, as variously demonstrated in other model systems. However, time-lapse imaging of planarians has proven to be a challenge. Especially the requisite immobilization of the animals over extended periods of time is difficult, owing to their photophobic behavior and soft body architecture. Here, we describe a new embedding method using 2% (w/v) low melting agarose, and demonstrate that this method can effectively immobilize animals as long as 7 days. In combination with cell-permeable fluorescent dyes, this immobilization method allows for the time-lapse imaging of planaria during regeneration and other physiological processes.