Not automatically. A quarter of the safe harbor amount is due at each deadline. Late installments earn interest unless your income arrived late the same way.
The safe harbor rule has two halves. The amount is 100% of last year's total tax, or 110% if last year's adjusted gross income was over $150,000. The timing is one quarter of that amount by April 15, June 15, September 15, and January 15. Form 2210 tests each installment on its own, so reaching the annual total in January does not undo three missed deadlines.
The penalty on the missed ones is interest at the IRS underpayment rate, currently 7% a year, on each shortfall for the days it was outstanding. Take a $10,000 safe harbor amount paid entirely on January 15. The April, June, and September installments of $2,500 were 275, 214, and 122 days late, and the three cost about $290 combined.
Two things remove the penalty. If your income arrived late in the year the same way your payments did, the annualized income method on Schedule AI resizes each installment to the income you had by that date, and the late payments can come out on time. And if the catch-up came through withholding rather than a payment, a raise in W-4 withholding or a large withholding election on a retirement withdrawal, Form 2210 treats it as paid in four equal parts on the due dates no matter when it was taken.
If neither applies, pay the balance now, file Form 2210 or let the IRS figure the penalty, and put the four dates on next year's calendar. The underpayment penalty calculator shows the figure for your own dates and amounts.
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Sources: Form 2210 instructions· IRS Publication 505