A synchronization system (100, 200, 400A, 400B, 600) for magnetic resonance (MR) systems includes a main magnet (104, 404, 692) having a main bore (113, 413) and opposed first and second ends (114); a system controller (110, 610) configured to generate a clock synchronization signal in accordance with a system clock; first and second transmission antennas (132,432, TX1, TX2) at opposite ends of the main magnet and configured to transmit the clock synchronization signal into the main bore of the main magnet; and a radio frequency (RF) portion (120, 660) including at least one reception antenna (136, RX1) and a synchronizer (122). The at least one reception antenna is situated within the main bore of the main magnet and is configured to receive the clock synchronization signal transmitted by the first and second transmission antennas. The synchronizer is coupled to the at least reception antenna and is configured to synchronize a clock of the RF portion in accordance with the received clock synchronization signal.