David Franks has been in the role since 2013
The CEO of Irish Rail will leave his role at the company in the coming months.
David Franks, who has been in his current role since February 2013, is set to take up a senior position in the public transport sector in Australia.
Mr Franks had previously been director of Keolis UK, the UK division of the French national railway company SNCF.
In a statement announcing Mr Franks' departure, Frank Allen - chairman of Irish Rail - said: "I want to thank David for his immense contribution to Iarnród Éireann over the past five years.
"David has led Iarnród Éireann at a very challenging time for the company and has delivered significant improvements in safety, passenger growth of 24%, and new customer-focused systems and processes. These changes will benefit the company for many years to come."
The recruitment process for a replacement is due to get underway shortly.
Mr Allen added: "I know David will remain fully committed to addressing the challenges the company faces in his remaining time with us."
The news comes less than 24 hours after it was announced that train drivers at Irish Rail have rejected a Labour Court recommendation on pay.
They voted by 83% to 17% to reject a recommendation over pay and productivity measures.
Iarnród Éireann said it "regrets the decision" by SIPTU and NBRU members.
The Labour Court had recommended a 1.15% pay increase to drivers, on top of a 7.5% increase to all employees over three years agreed last month.
Irish Rail workers held two 24-hour work stoppages last year before the Labour Court recommendations were issued.
The rail company had previously warned that pay rises could force it into bankruptcy.