William Joshua Allen was born on June 9, 1829 in Wilson County, Tennessee, United States. His father was Willis Allen, of Scotch-Irish descent, son of John Allen, who fell at New Orleans; his mother was Elizabeth Joiner, a North Carolina girl of Welsh descent. In 1830 Willis Allen migrated to the part of Illinois which later became Williamson County; he sat in the Illinois General Assemblies of 1838, 1844, and 1846 and served in Congress, 1851-1855, as a Democrat.
Allen studied law in his father's office and at Louisville, Kentucky, and then in the University of Louisville School of Law where he received a Bachelor of Laws degree in 1848.
Allen began the practise of law in 1849 at Metropolis, Illinois. In 1853 he removed to Marion, where he formed a partnership with John A. Logan, was elected to the General Assembly in 1854, and was appointed United States district attorney in 1855. His support of Stephen A. Douglas after the latter's break with the administration led the Attorney-General to seek excuse to remove him. Allen soon after resigned.
In 1859 he was elected judge of the circuit court succeeding his father in that office. Allen's course at the outbreak of the Civil War was equivocal. He endeavored to counteract the effect of a disunionist meeting held April 15, 1861, at Marion. By 1862 Allen was concerned in a movement to separate southern Illinois from the state and the Union and was an active Knight of the Golden Circle. He was arrested in August 1862, held prisoner for some months at Cairo and in the "Old Capitol Prison" at Washington and then released. In the summer of 1863 a local federal officer posted a guard on his residence. Allen was, however elected to the constitutional convention of 1862, to fill Logan's unexpired term in the Thirty-seventh Congress, and to succeed himself in the Thirty-eighth Congress (1863-1865). In 1864 he was beaten for reelection largely by the influence of his old associate, Logan, who returned from the army to denounce him for treasonable conduct. After the war, Allen practised first at Cairo, then at Carbondale, Illinois. He served in the constitutional convention of 1870, serving on the committee on the judiciary and as chairman of the committee on the bill of rights. In 1876 as special state's attorney he prosecuted those concerned in the Williamson Vendetta, which first gave the county the nickname of "Bloody Williamson. "
In 1886 he moved to Springfield and formed a partnership with C. C. and Stuart Brown.
In April 1887 he was appointed United States district judge for southern Illinois.
He died in Hot Springs, Arkansas on January 26, 1901.
Allen was a member of the Democratic Party.
In 1858 he married Anna McKeen of Maryland, who died August 17, 1892; three sons and two daughters survived them.
