The proposed schedule will see all primary school children offered the vaccine by 2016/17, and most secondary school children by 2018/19.
The plans were revealed in a letter from officials at Public Health England and NHS England to GPs and the wider NHS on Tuesday.
In February, it was announced that GP surgeries would offer the Fluenz Tetra vaccine to healthy four-year-olds for the first time from September. It followed the introduction of routine vaccination of two and three-year-olds last winter as the first step towards offering flu vaccination to all children aged two to 16.
Workforce 'a major challenge'
Now, officials have set out proposals for the full roll-out schedule over the next five years.
Under these plans, all five to 10-year-olds will be offered the vaccine by 2016/17, at which point all primary school children will be routinely offered the vaccine each autumn.
By autumn 2017/18, all 11 and 12-year-olds will also be offered vaccination, followed by the final addition of all 13 to 16-year-olds in 2018/19.
Vaccination for children aged five and over will be offered mostly through school-based programmes, with GP practices continuing to vaccinate two to four-year-olds.
Officials said significant changes to medical training were need in light of the huge vaccination programme, which will require around 1,000 full-time equivalent clinical staff upon full roll-out.
They wrote: 'Workforce capacity is a major challenge for implementation of this programme, which will ultimately see some 9m children offered vaccination in a short window every autumn.
'Local Education and Training Boards (LETBs) and area teams are currently developing their long-term plans to feed into the Health Education England workforce planning process. We encourage area teams and LETBs to ensure these plans take account of requirements for childhood flu immunisation.'
New flu 'taskforce'
A new National Flu Taskforce has been established to assist the programme, including commissioning and procurement support. The schedule remains provisional and will be kept under review each year.
Early findings from pilots to vaccinate schoolchildren aged four to 11 in 2013/14 suggest they may have reduced disease transmission and lowered demand on GP consultations, although low flu rates last winter meant the link was not statistically proven.
In 2012, the Joint Committee on Vaccination and Immunisation (JCVI) had recommended vaccination of all children aged two to 16 to reduce the burden of flu on the population.