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Separation is an important process in various fields in science and technology, and nano-structures are now being widely used to improve the resolution and speed of separation processes. Continuous separation occurs when the components of a mixture separate at different locations in a device; this makes it possible to inject a new sample into the device at any time during an on-going separation process. Continuous separation of nano-particles in a nano-channel composed of consecutive cones has been shown previously, while this study investigates whether a nano-channel can perform continuous separation of polymers such that polymers of different lengths are separated at the two sides of the channel. For this purpose, the motion of a charged polymer in an asymmetric nano-channel under constant and alternating applied electric fields was studied theoretically and by applying computer simulations. Theoretical formalism was used to determine the situation under which the channel could perform continuous separation, with computer simulations used to check the theoretical results. The effect of different channel parameters on the performance of the nano-channel, as a device for continuous separation, was thus determined.