James Ludlow spoke of his relief that exams have at least been cancelled so that students can be truly judged on their merits, but said more guidance was now needed on the way ahead.
It comes amid concern about the disparity between schools that have better resources than others and also individual students within schools, some of whom will have easy online access and others who may not be able to attend online classes.
The majority of pupils are now learning from home, however, schools are open for vulnerable children and children of key workers.
James Ludlow, principal at The King's Church of England School in Tettenhall, says he remains hopeful that the current lockdown will reduce coronavirus case numbers so that pupils can return to school as soon as it is safe to do so. It is hoped there may be some relaxation of the rules after February half term.
He called on the Government to now set out clear instructions on how schools should be working to ensure students missing GCSE and A-levels will be judged.
He said: " I believe it is the right decision to cancel the exams but it is vital that there is a clear plan for what will replace them. This plan is needed quickly. This uncertainty increases the pressure on our young people who have already had to cope with so much during this pandemic.
"The problem with doing any form of examined assessment this year is that there are big differences in the amount of lesson time that some pupils have missed compared to others.
"Added to this, there is the imbalance in how effectively pupils were able to learn whilst they were working from home during the first lockdown.
"It is likely that this will disadvantage certain sectors of the community more than others and will lead to an un-level playing field.
"There is so much at stake with our national exams and it is really important that the pupils are rewarded for their hard work with the grades they deserve."
Heads nationally have called for limits to the number of pupils in school during lockdown in England, with attendance rates in some schools surging up 50 per cent higher than in the first lockdown.
The two head teachers' unions, NAHT and ASCL, say the high numbers attending could hamper the fight against the virus.
It comes after the Department for Education widened the categories of vulnerable and key worker pupils who can attend.
The widened categories not only include vulnerable pupils and children of workers in critical occupations but also those who cannot access remote learning either because they do not have devices or space to study.
Mr Ludlow has said his school has not seen a big increase in number of pupils coming into school during the third lockdown and that it is coping well.
But elsewhere numbers are up, including at schools run by the Severn Academies Educational Trust (SAET), which says it has seen a 200 per cent increase overall in the number of key worker and vulnerable children attending.
Chris King, chief executive of the Trust, in Wyre Forest, said: “The numbers coming into our schools at the start of lockdown last March were quite low – for example on March 23, 12 pupils attended Hartlebury CE Primary, whereas there were 33 on January 11.”
The trust’s two secondary schools, Kidderminster’s Baxter College and Stourport High School, both started lockdown last March with fewer than 10 pupils and although the figure fluctuated. Last Monday they reported 37 and 36 pupils on-site respectively.
Mr King said the trust’s five primary schools were seeing an average of 22 per cent of their pupils on-site.