Hezekiah Niles was born in a Quaker farmhouse of the Jefferis family on October 10, 1777, as his parents escaped Wilmington, Delaware, from the invading British army under Lord Cornwallis. He lived with his older brother Samuel, and his mother Mary Way, who was a descendant of original Pennsylvania settlers. His father, Hezekiah, was a carpenter and plane maker, killed by a falling signpost outside his own workshop in 1790.Niles probably received his education at the Friends School in Wilmington. In 1794, he served in Philadelphia as an apprentice for printer, bookseller, and bookbinder Benjamin Johnson. Having been granted access Johnson's library, Niles engaged in extensive reading and built an interest in politics. Niles would often read before going to work, wherein he developed his expertise in becoming one of the fastest and most efficient typesetters in his day, a forte which he would carry throughout his printing career. While in Philadelphia, the U.S. Capital at the time, he often encountered prominent politicians on the street, such as George Washington. According to Norval Luxon, Washington "frequently seemed to give (Niles) an encouraging look...to which he would sometimes add a kind nod of recognition." Niles also contributed various articles dedicated to industrial development and Thomas Jefferson's election. His apprenticeship ended in less than three years when his employer's business went under.

Returning to Wilmington, Niles entered a printing business partnership for a couple of years with James Adams, Jr., son of Delaware's first printer. Inheriting much of the family estate when his elder brother Samuel died, he used the funds to begin another partnership selling books and printing, though the enterprise went into deep debt of over $25,000 within months. In 1798, Niles wed another Quaker named Anne Ogden, with whom he had 12 children, seven of which survived infancy. He went on to serve as Wilmington's town clerk and an assistant burgess, both for two terms, even serving positions within the Maryland Masons and the Baltimore Typographical Society. His first magazine, a literary composition called the Apollo or Delaware Weekly Magazine, ended after six months in 1805. In 1811, Niles briefly edited Post magazine in Baltimore, a publication supporting Jeffersonian ideals, but he soon sold it.

The Weekly Register became Hezekiah Niles' vision for a weekly, nationally-syndicated news magazine devoted to political discussion that offered more material than standard news magazines. At first a 16-page publication, Niles would expand its size to 24 pages, then 32, over the years. Said Niles in the Weekly Register about its content, it "has more of the pure characteristics of a newspaper than any other weekly print issued in the U. States" for containing the most public and government documents of the time, and so "the shape in which these things are presented has no reference to the character of them." The Weekly Register had a broad circulation around the country, with a wealth of prominent political leaders reading it and having over 3,000 subscribers within a year. The magazine was best known for its harsh ridicule of British foreign policy, with Niles often writing about his family's troubled experiences during the American Revolution, especially how British soldiers threatened his mother. In strong defense of fledgling American republicanism, Niles wrote in the Register that "man is the best able to govern himself, and that of a free republic is the strongest system yet devised for a social compact among men."

The Weekly Register, despite this opinionated and highly-patriotic delivery, still maintained balance and accuracy in its reporting, never endorsing or opposing candidates for office. Niles wanted the magazine open to all political persuasions, and he disallowed any carrying of advertisements so that his magazine would appear free from market influences. These editorial principles made the Register a key source for both economic news and protectionist theory in the early part of the 19th century. Niles took most of his information from other newspapers, skillfully condensing them to fit his magazine thanks to long working hours and forming a familial, dutiful connection with his readers. In gathering his source material, Niles was known to read over 4,000 letters per year.

Other views expressed by Hezekiah Niles' publication revealed more insight into his strong nationalist views: opposition to slavery, especially of slave trading within the country, and demanding a gradual abolition movement over time; opposition to "states' rights"; demanding steep tariffs on foreign imports, so as to strengthen domestic industry; supportive of expanding education; criticism of vigilante justice; a call for a greater amount of American-style literature and other publications; ridding postage from newspapers, so as to increase their circulation; promotion of tolerance for Latin America and calling for its liberation from Spain. In 1820, Hezekiah Niles would renounce all party affiliation, though he later called himself a Whig in opposition to Andrew Jackson's presidency. He wed his second wife, Sally Ann Warner, in 1826 after Anne Niles died in 1824. Together, they had eight children.

By the 1830s, Niles was subjected to a declining health because of his rigorous, self-imposed work schedule. He broke his arm in 1835 when falling from a carriage after the horses bolted, causing further strains on his writing abilities, followed by a paralyzing stroke a year later. Combined with rheumatism, he occasionally lost control of his writing arm from time to time. Despite these physical setbacks, Hezekiah continued his contributions to the Register, eventually having to dictate his writing, and he sometimes tried moving the paper while keeping his pen still in his hand. He surrendered the Weekly Register business to his son, William Ogden Niles, a few months afterwards. The magazine died out less than ten years later. Hezekiah Niles passed away early on April 2, 1839, at home in Wilmington, his family at his bedside.

Following Niles' death, The Baltimore Sun praised his magazine's contribution to the country, saying, "Such a man is a true patriot, and as long as the United States shall preserve its independence, so long shall the name of Hezekiah Niles...be revered, and his character quoted as an example for imitation, by all who desire to obtain that highest and noblest title: a good and honest man, in private life; in public; a pure disinterested patriot." The Daily National Intelligencer described Niles' character as "frank, honorable, independent, and truly republican spirit, simple in his manners, and habits, affectionate to his family, liberal to those who he employed in the prosecution of his business, disinterested and public spirited."