We searched for the $CP$-violating rare decay of neutral kaon, $K_{L} to pi^0 u overline{ u}$, in data from the first 100 hours of physics running in 2013 of the J-PARC KOTO experiment. One candidate event was observed while $0.34pm0.16$ background events were expected. We set an upper limit of $5.1times10^{-8}$ for the branching fraction at the 90% confidence level (C.L.). An upper limit of $3.7times10^{-8}$ at the 90% C.L. for the $K_{L} to pi^{0} X^{0}$decay was also set for the first time, where $X^{0}$ is an invisible particle with a mass of 135 MeV/$c^{2}$.