Eli Whitney Jr. was born in Westborough, Massachusetts, to Eli Whitney Sr., a prosperous farmer, and Elizabeth Fay. Early accounts suggest Whitney Jr. displayed a keen mechanical aptitude from a young age, showcasing skills in his father's workshop and demonstrating an innate ability to understand and manipulate machinery.

During his childhood and adolescence, Whitney demonstrated exceptional mechanical abilities. He reportedly disassembled and reassembled his father's watch, and during the Revolutionary War, he operated a profitable nail-making business from his family workshop. These early ventures hinted at his future entrepreneurial and inventive spirit, laying the foundation for his later pursuits.