The influence of shear flow on aggregation and disaggregation in aqueous solutions of the thermoresponsive methoxy-poly(ethylene glycol)-block-poly(N-isopropylacrylamide) (MPEG53-b-PNIPAAM113) copolymer that exhibits a lower critical solution temperature was investigated with the aid of turbidity, shear viscosity, and rheo small angle light scattering (rheo-SALS) methods. The turbidity results at quiescent conditions revealed a novel transition peak in the turbidity curve at intermediate temperatures, which reflects the delicate interplay between temperature-induced aggregation and shrinking of the species. A similar anomalous transition peak (located at the same temperature) was observed in the steady shear viscosity measurements at intermediate temperatures, and the amplitude of the peak was reduced with increasing shear rate as a consequence of breakup of interaggregate chains. At low temperatures (low sticking probability), enhanced shear rate generated interpolymer aggregates; whereas in the high-temperature domain (high sticking probability) association structures were broken up as the shear rate was increased. The rheo-SALS experiments disclosed growth of aggregates at low temperatures and destruction of association complexes at high temperatures. An increase of the cloud point temperature with rising shear rate is reported, which is interpreted as being a disruption of clusters under the influence of shear stresses.