In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome-wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other horse breeds, the LCORL/NCPAG locus on ECA3 showed the strongest association with withers height, but here we found that the best-associated SNP for that locus is nearly fixed in Friesian horses for the allele associated with small size. Moreover, we observed a clear decline followed by a marked increase in average withers height of the Friesian horse over time, probably owing to shifts in its primary use over the course of the years. Additionally, the frequency of the best-associated SNP on ECA1 has increased over time. Together, our study showed that ECA1 and ECA9 are associated with withers height in Friesian horses. Further studies should be performed to confirm candidate causal mutations.