Spin filtering requires a selective transmission of spin-polarized carriers. A perfect spin filter allows all majority (or minority) spin carriers to pass through a channel while blocking the minority (or majority) carriers. The quest for a novel low-dimensional metal-free magnetic material that would exhibit magnetism at a higher temperature with an excellent spin filtering property has been intensively pursued. Herein, using a first-principles approach, we demonstrate that the fluorinated boron nitride nanotube (F-BNNT) quantum dot, which is ferromagnetic in nature, can be used as a perfect spin filter with efficiency as high as 99.8%. Our calculation shows that the ferromagnetic spin ordering in F-BNNT is stable at a higher temperature. Comparison of the conductance value of the F-BNNT quantum dot with that of the pristine BNNT quantum dot reveals a significantly higher conductance in F-BNNT, which is in very good agreement with the experimental report (Tang, C., et al. J. Am. Chem. Soc. 2005, 127, 6552).