Werner was born on April 19, 1855 in Buffalo, New York, the son of German immigrants Peter and Margaret Werner.

In 1877, he moved to Rochester, and studied law in the offices of William H. Bowman, and later Dennis C. Feely.^[1] He was admitted to the bar in 1880. He was elected on the Republican ticket Special County Judge of Monroe County in 1884, was re-elected in 1887, and in 1889 was elected County Judge.

Werner was a justice of the New York Supreme Court (7th District) from 1895 to 1904, elected on the Republican and Democratic tickets.

In 1900, he was one of the first three additional judges designated^[2] to the New York Court of Appeals under the constitutional amendment of 1899.

In 1902, he ran on the Republican ticket for a regular seat on the New York Court of Appeals but was defeated by the incumbent Democrat John Clinton Gray.

In 1904, he ran again, this time in a cross-endorsement deal alongside Democrat Edgar M. Cullen on both the Republican and the Democratic tickets, and was elected.

In 1913, he ran on the Republican ticket for Chief Judge, but was defeated by Democrat Willard Bartlett. Werner remained on the bench as an associate judge and died in office.

Werner suffered from pernicious anaemia, and on February 9, 1916, had his spleen removed. He died a few weeks later at the General Hospital in Rochester, New York after pleurisy developed. He was buried at the Mount Hope Cemetery, Rochester.

• Court of Appeals judges at New York Court History
• GOVERNOR NAMES JUDGES in NYT on January 2, 1900
• The William E. Werner Collection with Bio, at Rochester Library
• JUDGE WERNER DIES AFTER AN OPERATION in NYT on March 2, 1916
• FUNERAL OF JUDGE WERNER in NYT on March 4, 1916