Born in Falmouth, Massachusetts, to John and Chloe (Thompson) Jenkins, Jenkins graduated Phillips Academy in 1868 and earned his Bachelor of Arts (A.B.) degree from Yale College in 1872. He pursued graduate studies at Yale's Sheffield Scientific School under the tutelage of noted agricultural chemist Samuel William Johnson. From 1875 to 1876, Jenkins studied in Germany at Leipzig University and then at the Royal Saxon Academy of Agriculture and Forestry in Tharandt, Saxony under Friedrich Nobbe.