East Renfrewshire and the Shetland Islands are also in the top five areas to be a girl in the United Kingdom, according to the study by Plan International UK.
However its State of Girls' Rights in the UK 2020 report highlights how regional inequality means some are growing up with greater rights and access to opportunity than others, and it calls for action to boost equality.
A survey for the report found six in 10 girls in Scotland (59 per cent) said they believe males are treated better than females in the UK.
More than half of the more than 1,000 girls and young women aged 14-21 surveyed in Scotland (56 per cent) said they have personally encountered a situation where they believe they would have been treated better if they were male.
She said: "As we enter 2020, it is encouraging to see that Scotland is leading the movement for giving girls greater access to opportunity and equality.
"But sadly our report finds that girls across the UK, including in Scotland, still feel disempowered and unable to realise their rights, with their potential largely determined by birthplace.
"Girls are told they can succeed, but they face a threat to their safety in public, online and in schools. They are told gender equality has been achieved, and yet they do not feel represented or heard by those in power.
"If adolescent girls are feeling undervalued, unheard and under-represented in public life, we as a society are letting them down. This simply cannot continue.
"The findings in this report should serve as a wake-up call for all politicians and leaders."
The city of Dundee is in the bottom 10 in the UK rankings, and is ranked last in Scotland.
Orkney is first while East Renfrewshire is second in the Scottish rankings, followed by the Shetland Islands, Aberdeenshire and Stirling.
The key findings of the report are that girls do not feel safe in public, still face inequality in the classroom, and that their voices are not being heard.
The study found girls' bodies are constantly scrutinised and stigmatised and cultural pressure to look a certain way remains a key source of anxiety in their lives.
The report outlines a series of recommendations to tackle the key challenges that girls face, including stopping street harassment, ending stigma around menstruation, and remodelling girls' experiences of school.
A Dundee City Council spokesman said: "Through the work of the Dundee Partnership, agencies and organisations in the city are working to make it a better place for everyone."
The top 10 places in Scotland to be a girl, according to the report, are:
1 Orkney Islands
2 East Renfrewshire
3 Shetland Islands
6 Perth and Kinross
7 Argyll and Bute
8 Scottish Borders
10 South Ayrshire
The bottom 10 are:
3 North Lanarkshire
4 North Ayrshire
5 East Ayrshire
7 West Dunbartonshire
9 Glasgow City
10 Dundee City.