We consider the unsteady flow of Burger fluid within a circular cylindrical tube, driven by a time-dependent pressure gradient, a body acceleration and a magnetic field acting normal to the flow direction. The solutions of the fractional constitutive equations governing the unsteady Burger’s fluid flow through arterial walls were obtained via the Laplace transform and the finite Hankel transform. The effects of magnetic field on parameters such as blood temperature and velocity were studied by Caputo time-fractional derivatives. We note that the solutions of many particular models such as fractional Oldroyd-B fluid, fractional Maxwell fluid, fractional second grade fluid and fractional Newtonian fluid models can be recovered from the solutions of the fractional constitutive equations governing the unsteady Burger’s fluid flow by particularizing the material coefficients (i.e. special and limiting cases of the earlier Burger’s fluid model). The numerical computations have been carried out to analyze the effects of fractional parameter α, similarity parameter β, relaxation time λ1, retardation time λ3, radius of the circular cylinder R0 and material parameter λ2 on the blood velocity and temperature. Some interesting flow and temperature characteristics are presented graphically and discussed. The study reveals that blood velocity, temperature and fractional parameters are reduced in the presence of magnetic field. The importance of this study can be found in the application fields of magnetic field control of biotechnological processes, bio magnetic device technology, biomedical engineering, medicine, etc.