He will succeed Ben Wells who will retire at the end of this year after a 46-year career.
Shepherd will report to chief executive officer John Chidsey and oversee Subway's global finance organisation, the company noted.
He will be responsible for managing and optimising the brand's global financial performance and information security.
Commenting on the appointment, John Chidsey, CEO, Subway, said, "Jeff has a well-earned reputation for driving strong financial results for global brands, bringing nearly 30 years of financial and accounting experience to our organisation.
"As we welcome Shepherd to Subway, we also thank Wells for his significant contributions.
"Since joining the company in December 2019, Wells has been a key driver of our brand's global financial stability and strategic growth, contributing to 11 consecutive quarters of positive sales results."
Wealth Of Experience
Shepherd joins Subway from Advance Auto Parts, where he served as executive vice-president and chief financial officer.
He was responsible for setting the financial strategy for the business and led the company's finance functions, including controllership and tax, financial planning and analysis, treasury, internal audit, pricing, and strategy.
Prior to this, Shepherd served as controller for General Motors Europe and held several senior roles within the organisation.
He also held a series of leadership roles with Ernst & Young where he developed a process for assisting global clients through bankruptcy and led tax remediation efforts.
According to Subway, Shepherd is based in the company's Shelton, Connecticut, headquarters and will work closely with Wells for the remainder of the year to ensure a seamless transition.