The fighters released a statement on Tuesday, saying: "Full control was taken last night over Qatabar directorate and control of all supplies and ammunition as well as buildings and other military sites."
Yemeni officials could not immediately be reached for comment.
Qatabar lies in the mountainous northern province of Saada, which borders Saudi Arabia, the world's leading oil exporter.
The northern province has also been the scene of most of the fighting that has taken place in recent months between Yemeni government forces and the rebels.
Saudi forces have also in recent days launched military strikes against the Houthis after the fighters killed a Saudi soldier in a cross-border raid last week.
Saudi officials said on Sunday that their forces had regained control of Jabal Dukhan, which was seized by the Houthi fighters.Saudi Arabia has become increasingly anxious about instability in Yemen, which is facing opposition from the Shia population in the north, separatist sentiment in the south and a growing threat from resurgent al-Qaeda fighters.
The 1,500km border between Yemen and Saudi Arabia is a security worry for the kingdom, which is building a high-tech border fence to prevent infiltration.
In the recent weeks, Houthi fighters have accused Saudi Arabia of allowing Yemeni forces to use its territory as a base to launch attacks against them and threatened to respond.
Al Jazeera's Hashem Ahelbarra, reporting from the Yemeni capital, Sana'a, said: "We are amid a campaign and a propaganda war with both sides saying they have made huge advances.
"Saudi Arabia is a key player in Yemen, it has loyalty of tribal leaders, politicians and religious leaders here.