Yves Desjardins-Siciliano is taking over from Steve Del Bosco, who had been doing the job on an interim basis since the start of this year.
Desjardins-Siciliano had been serving as Via's chief corporate and legal officer and corporate secretary since 2010.
A statement from Via says he has held executive positions in a variety of industries in Toronto and Montreal.
The appointment comes after Foreign Affairs Minister John Baird publicly demanded Del Bosco's head.
Baird said he lost confidence in Del Bosco because of how Via has been communicating with the public over issues like technical problems with safety equipment at rail crossings.
Baird, whose riding is in the national capital region, said the last straw came last month when Via wrongly accused Ottawa transit buses of causing a signal malfunction at a crossing near his home.
Del Bosco will be resuming his previous role as Via's chief commercial planning officer, the statement said.
Desjardins-Siciliano called it an "honour" to get the job.
"The task ahead is to ensure that inter-city passenger rail continues to play a key role in the economic prosperity of Canada," Desjardins-Siciliano said.
Via said last November that its overall ridership slipped two per cent to one million passengers in the third quarter of 2013, compared with the same period a year earlier.
However, it said ridership in the vital Quebec City-Windsor, Ont., corridor rose six per cent to 912,000.
Via operates intercity, regional and transcontinental trains linking 450 communities across its 12,500-kilometre route network, carrying almost four million passengers annually.