This study evaluated the suitability of time-of-flight secondary ion mass spectrometry (ToF-SIMS) to assess enamel fluoride uptake (EFU) in comparison with the microbiopsy technique. Enamel specimens were exposed to equimolar solutions of fluoride prepared from sodium fluoride (NaF), stannous fluoride (SnF2), or amine fluoride (AmF). EFU was quantified by both techniques on the same specimens. EFU was found to be highest for samples treated with AmF, followed by SnF2 and NaF. Both methods yielded clearly interpretable, highly correlating (r = 0.95) data. ToF-SIMS can be considered a promising alternative to the microbiopsy technique for near-surface EFU assessment.