We present high resolution near-infrared spectropolarimetric observations using the SPIRou instrument at CFHT during a transit of the recently detected young planet AU Mic b, with supporting spectroscopic data from iSHELL at IRTF. We detect Zeeman signatures in the Stokes V profiles, and measure a mean longitudinal magnetic field of $overline{B}_ell=46.3pm0.7$~G. Rotationally modulated magnetic spots likely cause long-term variations of the field with a slope of $d{B_ell}/dt=-108.7pm7.7$~G/d. We apply the cross-correlation technique to measure line profiles and obtain radial velocities through CCF template matching. We find an empirical linear relationship between radial velocity and $B_ell$, which allows us to estimate the radial velocity variations which stellar activity induces through rotational modulation of spots for the five hours of continuous monitoring of AU Mic with SPIRou. We model the corrected radial velocities for the classical Rossiter-McLaughlin effect, using MCMC to sample the posterior distribution of the model parameters. This analysis shows that the orbit of AU Mic b is prograde and aligned with the stellar rotation axis with a sky-projected spin-orbit obliquity of $lambda=0^{+18}_{-15}$ degrees. The aligned orbit of AU Mic b indicates that it formed in the protoplanetary disk that evolved to the current debris disk around AU Mic.
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