There were 2002 crimes recorded between April 2011 and March 2012 compared with 2113 in the previous year, a decrease of 5%.
Thefts of passenger property and public disorder offences fell but there was an increase in violent crimes on trains, with 384 attacks on passengers and staff recorded in the past year.
Chief Superintendent Ellie Bird said crime on the railways had fallen by over 30% in the past five years.
She said: "This has been another hugely successful year for BTP and the rail industry in Scotland which is seeing record passenger numbers. The sustained reduction in crime figures is a remarkable achievement and a tribute to our officers and the close working partnerships we have with our rail industry partners."