Julia Gallagher, who has been the headteacher at the school for two years, resigned earlier this month.
Mrs Gallagher took on the post in February 2014 - a year after the school, on Birchfield Road, was placed in special measures. Under her headship, the school was taken out of these measures last year.
The Trust has also issued notice of redundant roles, but does not expect staff to be made redundant.
A spokesman for the Isle Education Trust, (IET), which has been running the school since 2014, said: “It is with great regret that Isle Education Trust received Mrs Gallagher’s resignation earlier in the month.
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“She had led the school from its position post inspection of being in Special Measures to at it’s last inspection a ‘Good’ school. The curriculum development led by Mrs Gallagher has been of the highest possible order and leaves Epworth Primary Academy in a strong position to move forward.”
The Trust has refused to give the reason behind Mrs Gallagher’s resignation, but it comes at a time when the school is undergoing a restructure.
“As the Trust looks to grow, we have put in process, across all institutions, a consultation with staff in the areas of classroom support, IT support and estates to review these roles and responsibilities.
“In order to do this legally, IET has to operate in the same way as any other business organisation and has consulted with staff and their associated representatives.
“In order to be compliant, we have also had to issue notice of redundant roles. At this stage it is not envisaged by the Trust that any compulsory redundancies will be made. We would hope to have the process completed by mid June.
“The appointment of Mrs Gallagher’s successor is taking place this week, in order to secure a new principal for Epworth Primary Academy at the earliest possible opportunity and to ensure the standard of learning for children remains consistent.
“It is a reflection of the school’s reputation and the excellent work they do that the Trust has had such an overwhelming interest in this position. The Trust hopes to be able to release the name of the new principal in the early part of next week.”
A spokesman for Epworth Primary Academy said Mrs Gallagher was unwell and unable to comment.