It looked at the number of accidents recorded at each junction, then weighted the results according to the severity of injuries sustained and how many cyclists were active in the area.
The Arkleston Road/A761 junction in Paisley headed the list.
The charity, which promotes walking and cycling, said the results highlight the importance of better infrastructure.
The findings will be presented at the Scottish Transport Applications and Research conference this week.
Locations with dangerous junctions included Wallyford, Dundee, Tranent, Inverness and Stirling.
Roundabouts were featured in eight of the dangerous junctions, with seven others being T-junctions or staggered junctions.
Sustrans Scotland director John Lauder said: "Safety is often cited as the main reason why people don't cycle for more of the journeys they make every day.
"This research highlights the importance of having high-quality cycling infrastructure in place at junctions, so that collisions can be prevented.
"We know that better cycle infrastructure increases the feeling of safety and ultimately the number of people on bikes."
He added: "Put quite simply: the more people in a place who cycle, the safer it becomes for everyone."
Sustrans Scotland has been working with local authorities to address some of the specific concerns.
It contributed to a consultation on improving one of Edinburgh's busiest junctions, at Sheriffhall roundabout.
A Transport Scotland spokesman said: "The Scottish government remains committed to undertaking improvements at Sheriffhall roundabout having announced the preferred route option earlier this year.
"As part of the scheme, grade separation at Sheriffhall will improve access for pedestrians and cyclists compared to the existing arrangement.
"By allowing Edinburgh City Bypass traffic to pass over it will significantly reduce congestion and improve accessibility for all modes of transport including pedestrians and cyclists."
A list of the country's top 20 cycling collision hotspots has been drawn up by the charity Sustrans Scotland.