The optimization, manufacturing, and performance characterization of a miniaturized 3D receiver (RX)-based wireless power transfer (WPT) system fed by a multi-transmitter (multi-TX) array is presented in this study for applications in capsule endoscopy (CE). The 200 mm outer diameter, 35 μm thick printed spiral TX coils of 2.8 g weight, is manufactured on a flexible substrate to enable bendability and portability of the transmitters by the patients. The 8.9 mm diameter—4.8 mm long, miniaturized 3D RX—includes a 4 mm diameter ferrite road to increase power transfer efficiency (PTE) and is dimensionally compatible for insertion into current endoscopic capsules. The multi-TX is activated using a custom-made high-efficiency dual class-E power amplifier operated in subnominal condition. A resulting link and system PTE of 1% and 0.7%, respectively, inside a phantom tissue is demonstrated for the proposed 3D WPT system. The specific absorption rate (SAR) is simulated using the HFSS TM software (15.0) at 0.66 W/kg at 1 MHz operation frequency, which is below the IEEE guidelines for tissue safety. The maximum variation in temperature was also measured as 1.9 °C for the typical duration of the capsule’s travel in the gastrointestinal tract to demonstrate the patients’ tissues safety.