Upon passing the bar, Isaac, at age twenty-one, traveled west by steamboat to Saint Joseph, Missouri. 'St. Joe' was a bustling Missouri River port town, and offered many possiblities for a young lawyer, as the Ninth Missouri Circuit Court was held there. Isaac Parker's uncle D.E. Shannon, operated a legal firm in Saint Joseph with his partner H.B. Banch. In the firm of Shannon and Branch, Isaac began his legal career in earnest.
By 1861, he was operating on his own, working in the municipal and country criminal courts. The local courts afforded Parker not only experience, but community recognition. In April 1861, he won election to the post of city attorney as a Democrat. Just four days after Parker took office as city attorney, the Civil War began. The war caused Parker to reevaluate his political beliefs, and he broke with the Democrats, enlisting in a home guard unit, the 61st Missouri Emergency Regiment.
Parker married a Saint Joseph girl, Mary O'Toole, on December 12, 1861. He was reelected as city attorney in 1862 and 1863.
In 1864, Isaac Parker formally split from the Democratic party when he ran for county prosecutor of the Ninth Missouri Judicial District as a Republican. In the fall of 1864, he served as a member of the Electoral College, casting his vote for Abraham Lincoln.
In 1868, Parker sought and won a six-year term as judge of the Twelfth Missouri Circuit. The new judge gained experience and habits in this position that he would put to good use in the years to come.
Political ambition would catapult Parker from a Missouri judgeship to Congress in 1870.