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20 Oct. 1674, was son of Patrick Logan, a grandson of Sir Robert Logan of Restalrig. The father had joined the Society of Friends, and James was brought up in that religion. Before he was thirteen Logan had acquired some knowledge of Latin, Greek, and Hebrew, and he was at that age apprenticed to a linendraper; but on the landing of William III in Ireland his parents fled to Edinburgh, taking him with them, and afterwards settled in Bristol. Here he learnt French, Italian, and some Spanish, and by 1698 had begun to trade on his own account between Bristol and Dublin. He came to know Penn, who persuaded him to accompany him to Pennsylvania as his secretary. They sailed in September, and landed in Philadelphia in December 1699, and Logan lived in the same house in Second Street with Penn until the latter in 1701 finally returned to England. Logan was then made secretary to the province, commissioner of property, receiver-general and business agent for the proprietor, but also traded on his own account, the salary that he received being only 100l. a year. He maintained the interests of Penn, and subsequently those of his family, with ability and integrity against all opponents. He became a member of the provincial council in 1702, and remained one until 1747. In 1704 and 1705 Logan became embroiled in Governor John Evans's disputes with the assembly, and in the latter year he visited the Indians at Conestoga, after which he was always their staunchest friend. In 1706, when he was on the eve of departure for England on Penn's business, he was impeached on the charge of holding the surveyor-generalship and secretaryship simultaneously, and of tampering with the governor's commission. The dispute dragged on until November 1709, when his opponents obtained an order from the assembly for his arrest; but Governor Gookin issued a supersedeas on the grounds that Logan was a member of council and was going to England on the proprietor's business. Logan reached England early in 1710, and returned in 1712. In 1715 he was commissioned as a justice of common pleas, and in 1723 became presiding judge in that court and mayor of Philadelphia. At the conclusion of his year of office as mayor he again visited England to consult with Hannah, Penn's widow (Penn had died in 1718 and his eldest son in 1720). In 1725, after his return to Pennsylvania, Logan became involved in a controversy with Governor Sir William Keith, who was superseded in 1726. In the course of the dispute he published ‘The Antidote,’ Philadelphia, 1725, and ‘A Memorial from James Logan in behalf of the Proprietor's family and of himself, Servant to the said family,’ 1726. In 1728 Logan was maimed for life by a fall in which he broke off the head of his thighbone; but his energy was unabated. From 1731 to 1739 he acted as chief justice and as president of council, so that on the death of Governor Gordon in 1736 it fell to his lot to act as governor, and no new governor being appointed, he continued in the post for two years. After this he retired to Stenton, his seat near Germanstown, which is now a part of Philadelphia, where he devoted himself to scientific and classical studies, and where he died, 31 Oct. 1751. He was buried in the Friends' burial-ground, Arch Street, Philadelphia.

Logan married Sarah Reed, by whom he had four children, his eldest son, William (1718–1776), succeeding him as attorney for the Penn family, and devoting himself largely to agriculture and to the welfare of the Indians.

Logan defended Godfrey's claims to the invention of the quadrant, and was one of Benjamin Franklin's first protectors. In 1734 he communicated to the Royal Society ‘An Account of Thomas Godfrey's Improvement of Davis's Quadrant, transferred to the Mariner's Bow’ (Philosophical Transactions, xxxviii. 441), and about the same time began a correspondence with Sloane, then president of the society, and with Peter Collinson [q. v.] In 1735 he communicated to the latter an account of his experiment on the fertilisation of maize, an important demonstration of the sexuality of plants. This was published in the ‘Philosophical Transactions’ (xxxix. 192), and in an enlarged form as ‘Experimenta et Meletemata de plantarum generatione,’ Leyden, 1739. It was reprinted with an English translation by Dr. Fothergill, London, 1747. His ‘Charge to the Grand Inquest, 13 April 1736,’ Philadelphia, 1736, and London, 1737, a general disquisition on crime, and two letters to Sloane, ‘On the Crooked and Angular Appearance of Lightning,’ and ‘On the Sun and Moon, when near the Horizon, appearing larger,’ from ‘Philosophical Transactions,’ vol. xxxix., are reprinted in the ‘Memoirs’ of him published by Wilson Armistead in 1851. His translation of Cicero, ‘De Senectute,’ with preface and notes by Franklin, Philadelphia, 1744, is one of the best works issued from Franklin's press. It was reprinted in London in 1750 and 1778, in Glasgow in 1751 and 1758, and in Philadelphia in 1758 and 1812, these reissues falsely bearing Franklin's name.

Logan's other publications were: ‘Cato's Moral Distichs. Englished in Couplets,’ 1735,