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."

Spectators were joined by pagans and druids at the ancient monument in Wiltshire, but the dense cloud cover meant the sun remained hidden.
Police, who estimated 21,000 people attended, targeted the crowds with sniffer dogs and took 22 people into custody for drugs-related offences.
The solstice has had spiritual significance for thousands of years.
The word itself means a stopping or standing still of the sun.
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Find out more: BBC Religion Paganism
A crowd had gathered to spend the night near the giant stones, with police reporting 2,000 people on site by 21:30 BST on Thursday.
The sun then rose at 04:52 on the longest day of the year.
Supt Matt Pullen, from Wiltshire Police, said: "The majority of people respected the conditions of entry and the amnesty bins provided were used.
"Approximately 70 cannabis street warnings were issued. As with previous years, the passive drugs dogs proved very effective."
Twenty-two miles away (35km) at Avebury, where there are three stone circles, the crowd peaked at some 500 people.
BBC Radio Wiltshire reporter Rachel Royce said: "There are some very serious druids here in their long cloaks, taking it very solemnly. There are also some party-goers, and ordinary visitors who love the atmosphere.
"It really is a very peaceful and nice event."
A list of the country's top 20 cycling collision hotspots has been drawn up by the charity Sustrans Scotland.
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Thousands of people have gathered at Stonehenge for the sunrise on the longest day of the year.