The deficit went from £288.1m as at 3 March to £403.5m as at 1 September on an IAS 19 accounting basis.
The hospitality firm said the increase was down to the reduction in the discount rate from 3.70% to 2.20% and volatility in corporate bond yields following the referendum to leave the European Union.
Pension payments totalled £43.7m, down 38.9% on last year as the annual payment previously paid in August is now phased in equal monthly payments.
Further pension payments totalling roughly £45m are expected in the second half of 2016.
These payments are part of the agreed schedule of contributions which was based on the last triennial review in March 2014.
The recovery plan schedule of company contributions are £70m in 2016, £80m per annum for 2017 to 2021 and £7.6m in 2022.
Outside pensions, Whitbread saw strong growth, with total group sales increasing 8.1% to £1.6bn.
Core brands Premier Inn and Costa continued to win market share with total sales growing 8.9% and 10.7% and like for like sales up 2.4% and 2.3% respectively.
Whitbread chief executive Alison Brittain said: “This is another good set of results from Whitbread and we continue to deliver strong growth. Whilst it is early in the second half and there is uncertainty in the UK’s economic outlook, we expect to deliver in line with full year expectations.”
Chairman Richard Baker added: “Whitbread has delivered another good set of results with underlying profit before tax up 5.4%. We are continuing to invest in our brands to maintain our leadership positions, whilst our strong balance sheet and cash flow generation has enabled us to increase the dividend by 4.9% to 29.90p.”