Pugh was the son of a Chester County (Pennsylvania) Welsh-Quaker farmer-blacksmith, who died when the boy was 12. He learned blacksmithing, conducted an academy and used his inheritance to go to Europe at the age of 25. At Leipzig, where he studied chemistry, mineralogy, crystallography and physical geography, he began a lifelong friendship with Samuel W. Johnson, who shared his interest in experimenting with scientific agricultural education in the United States after seeing it in successful operation in Europe. Pugh went on to Goettingen, earning his Ph.D. in chemistry in 1856; studied at Bunsen's Heidelberg laboratory and in France; and then began research at the Rothamsted Experiment Station of Sir John Lawes in England. His work on the assimilation of nitrogen by plants won him international recognition and membership in the London Chemical Society. Johnson had returned to an agricultural chemistry professorship at Yale and later became the leader in the establishment of American agricultural experiment stations. Through him the trustees of the Farmers' High School approached Pugh about the presidency, which he accepted in 1859. The trustees authorized him to purchase laboratory equipment in Europe worth $1,500 of which he contributed $500 from his salary for the chemistry laboratory he designed and conducted in Old Main. He assumed his duties October 26, 1859, at the age of 31.