The rule operates independently of which physical or book-entry shares are actually delivered in the transaction. Modern brokerage accounts do not hold physically distinguishable share certificates for different purchase lots; shares of the same stock are fungible in the account. FIFO is a tax accounting convention layered on top of that fungible holding, assigning the earliest-acquired basis and holding period to the shares being sold, regardless of any operational detail about which shares moved. The rule answers a tax question, not a custody question.
The default has a predictable direction of effect in a market that has generally trended upward. Because the earliest lot was typically bought at the lowest price, in a stock or fund that has risen over time, charging a sale against that earliest lot typically produces the largest available taxable gain among the lots an investor holds. An investor who wants to minimize the taxable gain on a particular sale, or who wants to preserve a favorable long-term holding period on a specific lot, has to act before the sale by specifically identifying a different lot; simply doing nothing defaults into the outcome least likely to minimize the tax bill.
Since 2011, FIFO governs broker reporting as well as the taxpayer's own return, for covered securities. IRC 6045(g)(2)(B)(i) requires a broker to apply the first-in, first-out method for reporting adjusted basis on Form 1099-B unless the customer notifies the broker of an adequate identification, mirroring the taxpayer-facing rule in the Treasury regulation. This is why a broker's default cost-basis reporting on an ordinary stock sale, absent any specific instruction from the account holder, uses FIFO, and why the figure on a 1099-B will change if a customer gives the broker a specific identification before a sale rather than after.
FIFO also names a completely separate accounting method, and the shared name is a genuine source of confusion rather than a coincidence to wave away. In small-business and inventory accounting, first-in, first-out is a method for valuing cost of goods sold and ending inventory, assuming the oldest inventory items are the first ones sold to customers. The ordering logic, oldest first, is the same idea applied to a different subject. A securities investor reading about FIFO in the context of a small business's inventory, or vice versa, is reading about a related but distinct application of the same underlying convention, not about the stock-sale rule this page describes.
Choosing a different method requires acting before the sale, not after. The only way to avoid the FIFO default on a securities sale is specific share identification, made at the time of the sale and confirmed in writing by the broker afterward, which is covered on its own page. Once a sale has settled without that identification, FIFO has already applied, and there is no mechanism to retroactively substitute a different lot.