In 1850, Monahan was appointed Chief Justice of the Irish Common Pleas and held that office till 1876. He was generally agreed to have been one of the best Irish judges of his time: Elrington Ball states that during his long career he had the complete confidence of the Bar and the public, and it is notable that the Fenian trials of 1865-6 did not damage his reputation as they did that of his colleague William Keogh. He had the reputation of being "a thoroughly learned lawyer" but also one who brought strong common-sense to bear on a problem. Even Lord Westbury, the English Lord Chancellor, who disliked him, said patronisingly that Monahan "does know his law". Although he was impulsive and hot-tempered off the Bench, he was usually calm and controlled on it, and famed for his ability to "crush" counsel. Under stress according to one vivid description, he would "pace up and down the bench like a caged lion". He retired, due to failing health, in 1876, and died two years later. Of the civil trials he presided over the case which probably aroused the most interest was the Yelverton case, one of several cases heard in a number of countries where Major Yelverton, hoping to make a wealthy marriage, tried to rid himself of the inconvenience of his existing marriage to Miss Longworth. In Ireland initially he failed, as the lady's legal team convinced the jury that the marriage was valid. In his last years he, like most of his colleagues, was much troubled by the level of violent crime in Ireland, in particular the number of unsolved murders, many of them apparently linked to agrarian feuds. Addressing the Grand Jury of County Meath in 1870, he referred to several recent sensational crimes in the county, none of which had been solved, and remarked that he feared the country was enduring a "reign of terror".
Off the bench Monahan was a somewhat alarming personality : he was fierce in manner, impulsive, and give to peppering his conversation with swearwords. Lord Westbury, while grudgingly admitting his legal ability, referred to him disparagingly as "that voluble Irish savage". His many friends, however, insisted that his fierce manner concealed a genuine warmth of character. He married Fanny Harrington on 16 June 1832; they had two sons and six daughters, including James Henry Monahan, QC. The marriage was a happy one and Fanny's death was a great blow to her husband; during his last years he visited her grave at Glasnevin Cemetery each week.
