The influence of pulsed electromagnetic field therapy (PEMFT) on medium-sized vessels as well as capillary microcirculation is well known. Effects on lymphatic vessels, however, are difficult to visualize and have not been investigated to date. One of the operative treatment options in primary and secondary lymphedemas is lymphovenous anastomoses using supermicrosurgery. To prove patency of the anastomosis, the lymphatic flow is visualized by fluorescence using indocyanine green. The aim of this study was to investigate the influence of PEMFT on the lymphatic microcirculation, and compare it with conventional manual lymphatic drainage (MLD) during supermicrosurgery. Ten patients with lymphedema were included. Indocyanine green was injected before the operation for intraoperative visualization of the lymphatic vessels using a microscope equipped with an integrated near-infrared illumination system (Zeiss). The PEMFT system (Bio-Electro-Magnetic-Energy Regulation [BEMER]) was used as our standard device during a single 2-minute application period (AP) followed by MLD or vice versa. The mean light intensity in the calibration period (CP) was 46.53 ± 24.3 and 33.41 ± 12.92 for PEMFT and MLD, respectively. During the AP, the mean light intensity changed to 45.61 ± 24.40 for PEMFT and 57.05 ± 18.80 during MLD. This change between CP and AP did not differ significantly for the PEMFT application (p = 0.26), but showed an increase in light intensity during MLD (p < 0.001). We found a light intensity enhancement equivalent to a flow increase during MLD of 78.7% ± 45.7% (range 20%-144%) and no significant difference during the PEMFT application. A single period application of PEMFT did not affect the lymphatic flow.