During his tenure in the sheriff's office and the Legislature, he studied law, and was admitted to the bar.
In November 1888, Reilly was elected Clerk of New York County, and resigned his seat in the State Senate.
Reilly took office as County Clerk on January 1, 1889, but died in the middle of his three-year term.
He had suffered for some time from "a sort of malaria", and spent the summer of 1890 in Saratoga, the home of his wife.
In September he returned to New York City to attend to business, but died suddenly on September 28, 1890 at his home at 6 Attorney Street, from "typhoid fever".