Network Rail will be required to take on improvement projects on the Highland main line and between Aberdeen and Inverness.
£50m of the total sum will go towards securing national sleeper train services, with the UK government putting in the same amount.
Transport Minister Keith Brown said the infrastructural improvements would need to be matched by trains running on time.
He told parliament: "Scotland deserves a 21st century railway and this government will see it delivered."
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Mr Brown said the investment and targets would promote tourism and offer "real alternatives" to road and air travel.
The next rail contract will run for 10 years, longer than the current one, but has a potential five-year "break point", allowing the Government to terminate the arrangement.
The current £700m-a-year rail contract, held by FirstGroup, ends in 2014.
CBI Scotland said the proposals seemed "sensible" and thought businesses would “welcome” the investment.
But there was widespread criticism of the five-year contract "break" option.
Conservative Alex Johnstone said: "I believe a 10-year franchise is the minimum that's required in order to encourage a new franchisee to make the investment necessary to achieve the passenger comfort levels (the minister) mentions. But then he appears to make it clear he believes he can break that contract after five years - something which would undermine any attempt to encourage a new franchisee to invest."
(NE)
