Free bus travel was extended to everyone in Scotland aged under 22 earlier this year following a budget deal between the SNP and the Greens in Holyrood.
However, services which operate through the night “at a premium fare” are among those excluded in the legislation.
He said: “Young people are more likely to have jobs or social engagements that require them to travel home late at night so excluding the night buses from the free travel card is an odd decision.
“Sadly, we know that walking home late at night is not risk free, so removing the cost from these journeys could make a big difference.”
Mr Rennie accused SNP ministers of “just leaving this in the hands of already overstretched councils”.
Mary Kennedy, a student at Edinburgh University who raised the issue with Mr Rennie, said young people may decide to walk home instead of paying extra for a night bus.
The 18-year-old recently tried to use her free travel card to return to her student accommodation at around 1am.
She said: “When it is a premium service as well, I think a lot of people will just say, ‘Oh well, I’ll walk rather than pay the extra couple of quid.’
“Especially in a student place, there’s not exactly loads of money kicking about to pay the premium fare.
“It’s the difference between walking home alone, in the dark, at night, where vulnerable people are then at risk, compared to just getting on the bus and you’ve got people around you and you’ve got a bit of safety there. “
A single ticket in Edinburgh’s city zone costs £1.80 during the day and £3 at night, but fares are higher for journeys further afield.
In a letter responding to Mr Rennie, Ms Gilruth said the free bus travel scheme “will help strengthen our response to the climate emergency and support our green recovery by embedding sustainable travel habits in young people”.
She said: “As young people have been disproportionately impacted as a result of the Covid-19 pandemic, free bus travel will open up opportunities for them and improve their access to education, training and employment especially for those in low income households.
“Almost all registered local bus services in Scotland are eligible for the national concessionary travel schemes.
“However, some services which charge a premium rate, provide a special amenity, or services which are difficult to align with routine services and fare structures do not meet the criteria set out in the scheme legislation.
“Unfortunately that does include services which operate through the night at a premium fare.”
Ms Gilruth said Transport Scotland is “undertaking an evaluation which includes the consideration of personal safety and gender when traveling by bus, and we will be monitoring views on this, and any potential barriers to the scheme, over the course of the evaluation”.
She added: “Moreover, I have recently announced a focused engagement looking specifically at improving women’s experience and safety across public transport being taken forward by the Scottish Government.”