"Measurement of the neutral pion cross section in proton-proton collisions at $\sqrt{s}=200$ GeV with PHENIX" For the first time during the RHIC 2001--2002 run, the Relativistic Heavy Ion Collider at Brookhaven National Laboratory was successfully operated as polarized proton collider. The PHENIX detector triggered $4\times10^9$ p-p events at center of mass energies of $\sqrt{s} = 200$ GeV. We report the spin-averaged neutral pion cross section measurement in proton-proton collisions. Our measurement provides proton-proton reference data for the study of hadron production at high $p_T$ in heavy-ion collisions. We further compare our results with perturbative QCD calculations \cite{aversa} at next-to-leading order. A detailed experimental and theoretical understanding of hadron production in proton-proton collisions is essential not only for the heavy-ion physics program at RHIC but also for the study of polarized proton structure in polarized proton collisions at RHIC. The analysis uses the electromagnetic calorimeters in the two PHENIX central arms. A newly installed EM calorimeter trigger was essential in the detection of neutral pions at high $p_T$. We provide a detailed discussion of the systematic uncertainties of the measurement including the trigger bias, detector efficiencies and background estimates. \begin{thebibliography} \bibitem{aversa} Using the code from: F. Aversa, P. Chiappetta, M. Greco and J.-Ph. Guillet, Nucl. Phys. B327, 105 (1989). \end{thebibliography}