A method for preparing polybutene includes the steps of: supplying a C4 mixture to an isomerization reactor in which (i) 1-butene is isomerized into 2-butene by a hydrogen isomerization reaction using an isomerization catalyst in an isomerization zone of the isomerization reactor and (ii) iso-butene and 2-butene are separated by fractional distillation in a fractional distillation zone; supplying a C4 mixture containing 2-butene which is separated in the isomerization reactor to a skeletal isomerization reactor, in which a part of normal-butene is skeletal isomerized into iso-butene by a skeletal isomerization reaction using a skeletal isomerization catalyst, and the obtained skeletal isomerization mixture is supplied and recycled to the isomerization reactor; and supplying (i) a raw material containing the iso-butene of high concentration and which is separated from the isomerization reactor and (ii) a polymerization catalyst to a polybutene polymerization reactor and thereby producing polybutene by a polymerization reaction.