This paper is concerned with a system of heat equations with hysteresis and Navier-Stokes equations. In Tsuzuki (J Math Anal Appl 423:877-897, 2015) an existence result is obtained for the problem in a 2-dimensional domain with the Navier-Stokes equation in a weak sense. However the result does not include uniqueness for the problem due to the low regularity for solutions. This paper establishes existence and uniqueness in 2-and 3-dimensional domains with the Navier-Stokes equation in a stronger sense. Moreover this work decides required height of regularity for the initial data by introducing the fractional power of the Stokes operator.Mathematics Subject Classification. 47H05, 35Q35.