Underfloor heating is a common solution in single-family houses and a suitable solution for nearly zero-energy buildings as a low temperature heating system. According to general practice, the underfloor heating systems should be balanced to assure stable room temperatures and avoid under heating in rooms with higher heat losses. The purpose of the presented study was to analyze the effect of hydronic balancing on the room temperature fluctuations and heat pump performance. The tests were performed at full-scale nearly zero-energy building test facility with under floor heating and an air-to-water heat pump. We measured room and floor temperatures and monitored the heat pump electricity use and heat output. The heat balance of rooms was disturbed with internal gains introduced to several rooms in cycles. The results showed that room temperature fluctuations slightly increased of an unbalanced system, however during all tests, the average temperature fluctuations during night time were below 0.2 °C, so both systems performed well. We identified a negative effect of balancing on the heat pump performance as higher COP was measured in case of an unbalanced system. The results allow to conclude that in the case of studied system with one manifold and relatively small loop length differences the balancing had negligible effect on system performance. However, the topic should be studied further in more unfavorable conditions.