Accounts published by First Scotrail show the company made a profit of £14.2 million in the year ending March 31 2013, down from £17.3m in 2011/12.
The fall in profits came despite a 6.1% increase in income from passengers, from £280m in the 2011/12 to £297.4m in the most recent financial year.
However, the cost to Scotrail of raw materials and staff went up by almost £23m combined over the same period.
Meanwhile, turnover increased by about £165m to £778.7m, mainly as the result of a £150m increase in the Revenue Grant from the Scottish Government that covers the cost of track access charges levied by Network Rail.
The Revenue Grant for 2012/13 was £447m.
A spokesman for First said: "As planned, in 2012/13 ScotRail's track access charges paid to Network Rail increased significantly year-on-year to take into account network enhancements."