Carrier aggregation (CA) is a key enabling technique to increase the bandwidth of users in order to meet the increasing demand on peak data rates for emerging services and applications. However one of the main practical challenges that comes with CA is the severe increase in the peak-to-average-power ratio (PAPR) of the aggregated time domain NxSC-FDMA signal. This issue is critical for the user equipment (UE) in the uplink as it affects the efficiency of the power amplifier (PA) and hence the transmission coverage. In this paper, a novel two stage PAPR reduction scheme based on frequency spacing aware Discrete Fourier Transform (FSA-DFT) is proposed. Several CA scenarios were analyzed using the proposed technique. Experimental results show that the proposed technique provides a significant reduction in the PAPR of aggregated NxSC-FDMA signal.