It comes after the Joint Committee on Vaccination and Immunisation (JCVI) issued new advice following the latest review of data. Further advice on second doses will be given in the future.
Children will receive the Pfizer vaccine, which has been approved for use in the UK for people aged 12 and over.
It is understood officials are not ruling out vaccinations for otherwise healthy 12 to 15-year-olds but want to look at more information first.
All 16 to 17-year-olds will be able to register their interest for a vaccine on the mainland from Friday August 6, via the NHS Inform online portal. Those on the islands will be contacted by their health boards.
Appointments will be arranged soon, the Scottish Government said, with drop-in clinics also to be available. The starting date for these has not yet been given.
All will be offered an appointment by the end of September.
Chief Medical Officer Dr Gregor Smith said: “In line with the latest JCVI advice we will now be offering a first dose of the Covid-19 vaccination to young people aged between 16 and 17.
“The programme has always carefully assessed all the benefits and potential risks and offered vaccine to groups where this benefit is clear. The research and evidence shows that is the case for this age group and they should now be called forward for an appointment for a Covid-19 vaccine.
“We will continue to follow the expert JCVI advice and will await the outcome of analysis of data on second doses for this age group and any additional future advice on vaccination for those in the 12-15 age group.”
Appointments have already been extended to 12 to 17-year olds in Scotland who are particularly vulnerable, including those with underlying health conditions.
The JCVI said a number of factors had been considered in the new decision, which follows previous advice to offer vaccines only to vulnerable 12 to 17-year olds at first.
The most important element was the risk vs benefit of vaccination to the individual, the JCVI said.
Officials considered potential adverse reactions following vaccination, the frequency and severity of severe Covid in children and young people, the occurrence of Long Covid in children and the mental health and educational impacts of Covid, among other factors.
Experts from the JCVI as well as those from the Medicines and Healthcare products Regulatory Agency (MHRA) constantly review safety reports of the vaccine, from both the UK and abroad.
They said they considered reports of heart inflammation among some younger adults who had the jab, but officials said that this was considered to be “extremely rare”, affecting around one in 100,000 people vaccinated. And the effects are “mild” with a short recovery period.
Professor Wei Shen Lim, JCVI Covid-19 chair, said “After carefully considering the latest data, we advise that healthy 16 to 17-year-olds are offered a first dose of Pfizer-BioNTech vaccine.
“Advice on when to offer the second vaccine dose will come later.
“While Covid-19 is typically mild or asymptomatic in most young people, it can be very unpleasant for some and for this particular age group, we expect one dose of the vaccine to provide good protection against severe illness and hospitalisation.”
Dr June Raine, chief executive of the MHRA, said the decision came following “rigorously reviewed” trials in children and young people.
Dr Raine said: “All of this shows (the vaccine) is effective in the same way as we see in adults aged 16 to 25.”
She added: “This meant that the vaccine could be approved for use in young people aged 12 to 15 years.”
“The safety data and adolescence was comparable to that we’ve seen in young adults and no new adverse events were identified.
“As in young adults, the safety profile showed mild to moderate reactions in line with the way the vaccine works, perhaps of temperature, sore arm, headache – that kind of thing.”
Professor Rowland Kao, Chair of Veterinary Epidemiology and Data Science at Edinburgh University, said vaccination of teenagers could reduce the risk of severe Covid illness, which is lower but still present.
He added that vaccination should reduce disruption in schools, and help to reduce overall Covid spread as there is evidence that older children can perpetuate chains of transmission.
The Scottish Government and opposition parties welcomed the new advice.
First Minister Nicola Sturgeon said vaccines will be offered to 16 and 17-year olds “as soon as possible”.
Health Secretary Humza Yousaf said: “Vaccination continues to be the best way to protect yourself and those around you and I urge anyone who is eligible to take up the offer of the vaccine.
“The national vaccination programme has been a huge success and without doubt, represents our best way out of the pandemic.”
Scottish Greens MSP Gillian Mackay said: “With schools begging to return from the summer holidays next week, and colleges and universities starting their new terms next month it is important that the Scottish Government begins offering these vaccinations as quickly as possible.“It’s essential that access to vaccination is made as easy as possible. So, I’d encourage ministers to take the vaccine to young people, increase the number of pop up sites and drop in centres and ensure that students can access on campus vaccination.
“I’m sure that many young key workers, particularly in sectors like retail and hospitality, will be relieved that they will now be eligible for the same protection that was previous limited to their older colleagues and customers. It’s now vital that government commences this rollout urgently.”