We developed and built a new system of readout and trigger electronics, based on the waveform digitization and pipeline readout, for the KOTO experiment at J-PARC, Japan. KOTO aims at observing the rare kaon decay KL → π0νν̅. A total of 4000 readout channels from various detector subsystems are digitized by 14-bit 125-MHz ADC modules equipped with a 10-pole Bessel filter in order to reduce the pile-up effects. The trigger decision is made every 8-ns using the digitized waveform information. To avoid dead time, the ADC and trigger modules have pipelines in their FPGA chips to store data while waiting for the trigger decision. The KOTO experiment performed the first physics run in May 2013. The data acquisition system worked stably during the run.