Giraffe, one of only three or four blockade runners owned by the Confederate government, was renamed R.E. Lee. All other blockade runners were privately owned and were so profitable that often one successful trip would more than pay for the loss of a ship. "A blockade-runner," Tabb once wrote, "was almost as invisible at night as Harlequin in the pantomime. Nothing showed above the deck but two short masts, and the smokestack; and the lead-colored hull could scarcely be seen at the distance of one hundred yards. Even on a clear day they were not easily discovered."

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Sailors on the privately owned ships were paid $100 a month in gold and a $50 bonus at the end of a good trip, which usually took about seven days. The crews of the government-owned blockade runners were paid the same. Captains and pilots earned as much as $5,000 a year. Navy captains, subordinate officers and pilots received only the pay of their rank in gold.

R.E. Lee became one of the most famous of all the blockade runners. She ran the blockade 21 times, with 6,000 to 7,000 cotton bales worth $2 million in gold, and she brought back cargos of equal value. Tabb served aboard until almost the end of her Confederate service. The voyages were between Bermuda or Nassau and such Carolina coastal cities as Wilmington, Beaufort and Charleston. Tabb said that on each trip they had to pass through 20 to 30 Federal warships, and that the task was not made easier when the cargo was ammunition.

During one trip, bad weather forced R.E. Lee to stray off course, and she met a Federal blockader too suddenly for evasive action. The quick-witted Captain Wilkinson ordered the ship quickly rigged to impersonate a Federal transport (many captured blockade runners were converted to that use). He ran up the United States flag, saluted the blockader, who returned the salute, and proceeded on his way.

On another occasion, more aggressive action was necessary. Outbound for Nassau, R.E. Lee was chased by USS Iroquois, a sailing vessel. She had government gold in her cargo and was using inferior coal, which was costing her speed. Cotton bales were quickly soaked in turpentine and used as fuel, and the boilers were fired so high that the deck was almost scorching hot. R.E. Lee stayed ahead of her pursuer and, at dusk, put up a smoke screen, made a sharp 90-degree turn and escaped.

In September 1863, Wilkinson was put in charge of an expedition to free Confederate prisoners of war at Johnson's Island, near Sandusky, Ohio. A party of handpicked men was formed, with Lieutenant Robert Minor as second-in-command. The inclusion in the party of young Johnny Tabb was evidence of the high esteem in which his commander held him.

The expedition was a true cloak-and-dagger affair. The party, including a replacement captain for R.E. Lee, sailed for Halifax, Nova Scotia, on October 10, 1863, with a cargo of cotton. She was attacked and struck by enemy fire while running the blockade, but got through with only minor damage. The proceeds from the sale of the cotton were to be used to buy blankets and shoes for the army and for the needs of the released prisoners. The men arrived in Halifax on October 16, and because such a large party of Confederates would attract attention, they split into small groups. Wilkinson had been given letters to certain individuals in Canada who were ready to help, and an advance man was sent to Montreal, via Portland, Maine, to advise them of the party's coming.

The party got as far as Toronto, but the plot was discovered and the Canadian governor general issued a proclamation threatening to imprison anyone violating his country's neutrality laws. He also notified United States authorities, and the prison garrison was reinforced and placed on full alert. The expedition was therefore called off, and the entire party returned to Halifax, making part of the trip by sleigh, and booked passage on Alpha, the first steamer available bound for Bermuda, in December 1863.

R.E. Lee, under her replacement captain, sailed from Halifax after landing the expedition party. She was captured off the North Carolina coast on her way to Texas with army payrolls. Renamed Fort Donelson, she was assigned to Union blockade duty and subsequently participated in the capture of Fort Fisher and the closing of Wilmington, the last port open to the Confederacy–an ironic ending to the career of a famous blockade runner.

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