As a Congressman, Long had become a close friend of William McKinley, who was elected President in 1896.
McKinley offered Long his choice of several cabinet posts; he chose Secretary of the Navy.
He was confirmed by the United States Senate on March 2, 1897.
The appointment brought on a storm of criticism from Henry Cabot Lodge.
Lodge had been elected to the Senate, dominated the Republican Party in Massachusetts, and had expected to have a say in choosing a cabinet nominee in return for his support of McKinley.
One of Lodge's supporters complained that Long was in poor health, and that he would not give the administration "back-bone and vigor". (
Long had back from his law practice after a nervous breakdown.)

Lodge compensated for the setback by helping secure the position of Assistant Secretary for Theodore Roosevelt, a brash and aggressive New Yorker.
Long and Roosevelt did not get along: in addition to personality differences, Roosevelt pushed a view to aggressively modernize and expand the Navy against Long's more studied and conservative approach.
He preferred to expand the Navy gradually.
As the nation's global interests grew, Long committed himself to the nation's peaceful growth in line with McKinley's policies.
As a result of his disagreements with Roosevelt, Long took steps to control his subordinate.
Roosevelt, on the other hand, sought ways to spur Long into action, writing "I only wish that I could poison his mind so as to make him a shade more truculent in international matters".
He also chafed against Long's policy of deferring much of the department's work to its permanent bureau chiefs, which resulted in constraints on the flow of information the administration received.
Long was somewhat proud of the fact that he knew little of the detail of naval affairs, commenting that he was "a civilian who does not know the stem from the stern of a ship".

Long believed that ongoing tensions between Spain were unlikely to lead to war, and should it, that the war would be easily won.
He consequently did not take significant steps to prepare the Navy for that contingency.
In January 1898, he ordered the USS Maine to Havana, Cuba, as a matter of "customary relations".
He and McKinley were concerned for the safety of Americans in Cuba due to the ongoing Cuban War of Independence.
By early February 1898, tensions had reached crisis proportions, and Long was compelled to begin drawing up plans for war.
The explosion and sinking of the Maine at Havana on February 15 was the spark that ignited the Spanish–American War.
The administration was opposed to war, but the public outcry over the sinking could not be ignored.
Ten days after the sinking, Long took a day off, and Roosevelt used his authority in Long's absence to issue a number of orders designed to increase the Navy's readiness for war, including famously ordering Commodore George Dewey into an aggressive offensive posture in the Spanish Philippines.
Long countermanded some of Roosevelt's orders afterward, but began stepping up naval war preparations.

The loss of the Maine highlighted to the administration the nation's shortage of modern warships, setting off a scramble for the acquisition of more ships.
One significant order given by Long was to transfer the USS Oregon (one of the Navy's most powerful ships) from the west coast to the Caribbean; the ship made the journey around Cape Horn from San Francisco to Key West, Florida, in 66 days.
War was declared in April 1898.
Roosevelt resigned his post the next month, a move Long thought foolhardy but later acknowledged was significant in advancing Roosevelt's career.

Long directed the Navy's activities throughout the war, significantly increasing its size in the process.
He ordered Dewey to neutralize the Spanish fleet in the Philippines, ordered the seizure of Spanish Guam, and worked to support a blockade and offensive operations against Cuba.
He also directed naval resources into threatening postures against mainland Spain to encourage the Spanish recall of a fleet destined for the Philippines.

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As a Congressman, Long had become a close friend of William McKinley, who was elected President in 1896. McKinley offered Long his choice of several cabinet posts; he chose Secretary of the Navy. He was confirmed by the United States Senate on March 2, 1897. The appointment brought on a storm of criticism from Henry Cabot Lodge. Lodge had been elected to the Senate, dominated the Republican Party in Massachusetts, and had expected to have a say in choosing a cabinet nominee in return for his support of McKinley. One of Lodge's supporters complained that Long was in poor health, and that he would not give the administration "back-bone and vigor". (Long had back from his law practice after a nervous breakdown.)
Lodge compensated for the setback by helping secure the position of Assistant Secretary for Theodore Roosevelt, a brash and aggressive New Yorker. Long and Roosevelt did not get along: in addition to personality differences, Roosevelt pushed a view to aggressively modernize and expand the Navy against Long's more studied and conservative approach. He preferred to expand the Navy gradually. As the nation's global interests grew, Long committed himself to the nation's peaceful growth in line with McKinley's policies. As a result of his disagreements with Roosevelt, Long took steps to control his subordinate. Roosevelt, on the other hand, sought ways to spur Long into action, writing "I only wish that I could poison his mind so as to make him a shade more truculent in international matters". He also chafed against Long's policy of deferring much of the department's work to its permanent bureau chiefs, which resulted in constraints on the flow of information the administration received. Long was somewhat proud of the fact that he knew little of the detail of naval affairs, commenting that he was "a civilian who does not know the stem from the stern of a ship".
Long believed that ongoing tensions between Spain were unlikely to lead to war, and should it, that the war would be easily won. He consequently did not take significant steps to prepare the Navy for that contingency. In January 1898, he ordered the USS Maine to Havana, Cuba, as a matter of "customary relations". He and McKinley were concerned for the safety of Americans in Cuba due to the ongoing Cuban War of Independence. By early February 1898, tensions had reached crisis proportions, and Long was compelled to begin drawing up plans for war. The explosion and sinking of the Maine at Havana on February 15 was the spark that ignited the Spanish–American War. The administration was opposed to war, but the public outcry over the sinking could not be ignored. Ten days after the sinking, Long took a day off, and Roosevelt used his authority in Long's absence to issue a number of orders designed to increase the Navy's readiness for war, including famously ordering Commodore George Dewey into an aggressive offensive posture in the Spanish Philippines. Long countermanded some of Roosevelt's orders afterward, but began stepping up naval war preparations.
The loss of the Maine highlighted to the administration the nation's shortage of modern warships, setting off a scramble for the acquisition of more ships. One significant order given by Long was to transfer the USS Oregon (one of the Navy's most powerful ships) from the west coast to the Caribbean; the ship made the journey around Cape Horn from San Francisco to Key West, Florida, in 66 days. War was declared in April 1898. Roosevelt resigned his post the next month, a move Long thought foolhardy but later acknowledged was significant in advancing Roosevelt's career.
Long directed the Navy's activities throughout the war, significantly increasing its size in the process. He ordered Dewey to neutralize the Spanish fleet in the Philippines, ordered the seizure of Spanish Guam, and worked to support a blockade and offensive operations against Cuba. He also directed naval resources into threatening postures against mainland Spain to encourage the Spanish recall of a fleet destined for the Philippines.
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John Davis Long