The FCA made a loss of £58.3m in the year to 31 March 2015, its annual report shows.
This compares to a £29.3m loss in 2013/14.
The FCA says the figure is in line with expectations and has been driven by a larger loss in its defined benefit pension scheme, plus consumer credit costs.
The regulator says it made an actuarial loss of £33.4m relating to its DB scheme.
This compares to an actuarial loss of £26.4m in 2013/14, after its discount rate fell from 4.40 per cent to 3.40 per cent over the year.
The FCA says it is running a deficit of £24.9m, primarily caused by the timing delay between set-up costs of £30m incurred during the year for consumer credit activities and the recovery of these over a 10-year period.
FCA fines totalled £1.42bn in 2014/15, up from £432.1m in 2013/14.
Of this, £1.36bn was paid to the Treasury. A deduction of £42.6m is made by the regulator to cover enforcement costs, which it says will be returned to fee payers in the following year.