The Foundation offers Fremantle Hospital-based researchers five types of Awards:

The Fremantle Hospital Research Awards - each year medical research teams are invited to apply for seed funding of up to $15,000 for projects which may be in any area of medicine.

The Warren Jones Awards - comprising a Scholarship half-funded by the University of Western Australia which will allow high calibre students to undertake PhD studies under the supervision of senior researchers based at Fremantle Hospital; a Fellowship which will be a residency by a high quality Post-Doctoral researcher of up to 84 days with the intention of assisting skills transfer to researchers at Fremantle Hospital; and an annual Oration.

The Barry Marshall Travel Award - which will allow a researcher to attend a national or international conference to present their research findings.

The Fremantle Hospital Equipment Award - this occasional Award of $10,000 will be presented to a team of researchers who are best able to demonstrate the need for a piece of research equipment that will be of the greatest benefit to a large number of research personnel/patients.

In 2012, two new awards "Excellence in Publicaitons" will be made. One award of $5,000 will be made to a senior member of staff and the other award, of $2,500, will be made to a less senior member of staff.