Paynter first became involved with West Ham as unpaid help from 1897. In the 1900-01 season Paynter joined West Ham United. However, he never played for the first-team and in a match against Woolwich Arsenal he sustained a knee injury which ended his career.
The club appointed him reserve-team trainer in 1902. He was then promoted to first-team trainer when Syd King, the previous holder of the position, was appointed as the first team manager.
When King was sacked in 1933 Paynter was chosen as his replacement. Paynter remained the manager of West Ham United until 1950.