The transport group wrote down the value of its aviation business by 38 million last year as cargo volumes plunged.
Govia, the rail joint venture majority owned by Go-Ahead, also suffered from the downturn in air travel, as fewer passengers used the Gatwick Express service, which links the airport with central London.
Chief executive Keith Ludeman said that, while there had been some signs of a recovery in aviation volumes in the last two months, trading in the sector remained challenging.
"Aviation has had an extremely difficult year," he said.
Go-Ahead's aviation business, which handles cargo and passenger baggage at 15 airports across Britain, suffered a 20 per cent fall in revenue last year, and made a 4.5m operating loss.
However, excluding the aviation business, Go-Ahead said its business had been largely resilient during the recession, as it reported better than expected underlying pre-tax profits of 112.1m in the year to 27 June, on revenue up 6.7 per cent to 2.35 billion.
Rail, which accounts for more than two-thirds of the group's turnover, saw an increase in revenue as it took on new services, but operating profits at the business dropped 20 per cent to 61.5m.
Ludeman said that passenger numbers using its three rail franchises had been "pretty robust", although there had been a fall in the numbers of commuters coming into the City.
All of Go-Ahead's rail franchises – Southern, South Eastern and London Midland – carry commuters into London.
The strongest business remained its bus division, which carries an average of 1.6 million passengers a day.
With a strong share of the London-market, the business increased both its revenue and operating profits, despite rising fuel and pension costs.
Go-Ahead's bus business also had to overcome a writedown related to the removal of "bendy" buses from the streets of London. Mayor of London Boris Johnson pledged to phase out the articulating single-deck buses as part of his election campaign, claiming they are dangerous to cyclists and pedestrians.
Go-Ahead said the phased withdrawal of the buses meant it was being forced to increase the rate of depreciation on the vehicles. The group plans to make phased writedowns of 4m over the next three years, including an 800,000 hit taken in yesterday's results.
The company proposed a final dividend of 55.5p, meaning its total dividend will be 81p, the same level as in 2008.
Its shares closed up 5.2 per cent at 1,371p.