The girl died in Coventry's University Hospital on Monday lunchtime after being given the Cervarix jab at the Blue Coat CofE school in Coventry.
The batch of the vaccine used has been placed into quarantine as a precaution.
Dr Caron Grainger, joint director of public health for NHS Coventry and Coventry City Council, said: ‘The incident happened shortly after the girl had received her HPV vaccine in the school. No link can be made between the death and the vaccine until all the facts are known and a post mortem takes place.
‘NHS Coventry has taken the proactive step to quarantine the batch of vaccine being used as a precautionary measure only and has informed the regulatory authority. We are conducting an urgent and full investigation into the events surrounding this tragedy.'
Since September 2008 there has been a programme in England to vaccinate girls aged 12-13 against HPV. There is also a three-year catch-up campaign that will offer the HPV vaccine to 13-18 year-old girls.
Dr Pim Kon, medical director of Cervarix's manufacturer GlaxoSmithKline UK, said: 'Our deepest sympathies are with the family and friends of the young girl.
'We are working with the DoH and MHRA to better understand this case, as at this stage the exact cause of this tragic death is unknown.'
She added that more than 1.4 million doses of Cervarix have been given as part of the immunisation programme. The vast majority of suspected adverse reactions reported to the MHRA in association with Cervarix have related either to the signs and symptoms of recognised side effects listed in the product information or were due to the injection process and not the vaccine itself.