In areas with low seismic activity, such as Northern Hokkaido, Japan, site amplification factors are evaluated based on limited number of seismograms. In this case, the evaluated site amplification factors are quite dependent on the characteristics of individual records. Although site amplification factors at 260 strong-motion sites in Hokkaido were evaluated by Nozu and Nagao (2005), it was found afterword that the site amplification factors at several sites, most of which are located in Northern Hokkaido, are overestimated at around 0.2 Hz due to inadequate characteristics of the records. Therefore, in this study, site amplification factors for strong-motion sites in Northern Hokkaido were re-evaluated based on currently available strong motion data using spectral inversion technique. In the analysis, records from four earthquakes at 118 sites were used. To avoid the trade-off between the source characteristics and the site amplification factor, the site amplification factors at three sites were constrained using the results of Nozu and Nagao (2005). As a result of the analysis, the site amplification factors at 115 sites were newly obtained. It can be recognized that the new results are free from the overestimation around 0.2 Hz which was found in the results of the conventional analysis (Nozu and Nagao, 2005). For the majority of sites and frequencies, the newly obtained site amplification factors are in agreement with the results of Nozu and Nagao (2005). In the west of Northern Hokkaido, where thick sediments are located, the evaluated site amplification factors are large in the low frequency range (0.2 - 1 Hz). The source characteristics estimated in the analysis are in good agreement in the low frequency range with the F-net CMT solutions, indicating the adequacy of the constraint used for the inversion.