Trifluoroacetic anhydride is widely used in organic synthesis as a powerful reagent for introducing the trifluoroacetyl group. It is commonly employed in the preparation of trifluoroacetyl derivatives of amines, alcohols, and other nucleophiles, which are useful intermediates in pharmaceutical and agrochemical synthesis. Due to its high reactivity, it facilitates efficient acylation under mild conditions.

It is also used in peptide chemistry to protect amino groups temporarily, as the trifluoroacetyl group can be removed under mild basic or acidic conditions. In addition, TFAH serves as a dehydrating agent in the formation of nitriles from aldoximes and in the synthesis of heterocyclic compounds.

In analytical chemistry, it is applied in derivatization procedures for enhancing the volatility and detectability of polar compounds in gas chromatography-mass spectrometry (GC-MS). Its strong electrophilic nature makes it effective in activating carboxylic acids for subsequent coupling reactions.

Due to its moisture sensitivity and corrosive nature, handling requires care, typically under anhydrous conditions and in fume hoods with appropriate protective equipment.