He was appointed to the Continental Navy Board on November 6,1776. It was while serving on the Continental Navy Board that he turned his attention to designing the flag of the United States. The use of stars in that design is believed to have been the result of an experience in the war directly related to his property.

A book in Hopkinson's library at his home in Bordentown was taken by a Hessian soldier in December 1776, a dark year of the war. The book, Discourses on Public Occasions in America (London, 1762) by William Smith, D. D., had been a gift to him by the author. The soldier, one I. Ewald, wrote on the inside cover that he had seen the author near Philadelphia and that he, Ewald, had taken the book from a fine country seat near Philadelphia. The book was subsequently given to someone in Philadelphia who returned it to Hopkinson. The soldier had written above and below Hopkinson's bookplate, which had three six pointed stars and his family motto, "Semper Paratus", or "Always Ready". The safe return of the book may well have symbolized to Hopkinson the revival of the Americans hope.

In a letter to the Board of Admiralty in 1780 Hopkinson asserted that he had designed "the flag of the United States of America" as well as several ornaments, devices, and checks appearing on bills of exchange, ship papers, the seals of the boards of Admiralty and Treasury, and the Great Seal of the United States. Hopkinson had received nothing for this work, and now he submitted a bill and asked "whether a Quarter Cask of the public wine" would not be a reasonable and proper reward for his labors.

The Board forwarded the letter to Congress, which referred it to the Board of Treasury. Apparently acting on a request from Congress, Hopkinson sent a detailed bill on June 6th, and it was sent to the auditor general, James Milligan. He sent it to the commissioners of the Chamber of Accounts, who replied six days later on June 12th that they were of the opinion that the charges were reasonable and ought to be paid. Milligan gave the report a favorable endorsement and passed it on to the Board of Treasury. The board now raised objections and returned the bill to the auditor general on the grounds that no vouchers were included with the bill. Hopkinson now submitted a new copy of his bill and itemized each charge and it was rejected once again, and the auditor asked once more for its favorable consideration. After another round of referral through the departments, the board filed the correspondence and did nothing for two and half months.

Fed up with the delay, Hopkinson wrote to Charles Lee, the secretary of the Board of Treasury, accusing him of lying about having received the amended bill and delaying the settlement of his claim. Lee failed to satisfy Hopkinson, and the latter sent to Congress a list of charges against the board.

Just as in our modern times, Congress appointed a committee to investigate the matter. The various government officers concerned with the claim appeared before the committee at its request. Only the men of the Board of Treasury ignored the summons. In its report to Congress, the committee recommended that the present board be dismissed.

Congress sent the report back to the committee for further consideration and another investigation and another report followed. In its second report the committee noted that this time the members of the Board of Treasury answered the summons, but frequently tried to dictate the way in which the investigation should be made. The committee felt that the Treasury should be directed by a single individual responsible to Congress, but made no recommendation in regard to Hopkinson's claim. The matter remained unsettled until August 23rd,1781, when Congress passed a resolution asking that the claim be acted on. Meanwhile, Hopkinson had grown weary of the controversy and on July 23rd, 1781, he resigned his office as Treasurer of Loans. One of Hopkinson's chief opponents on the board of Treasury resigned the same day.

Between the first and second report of the committee the Board of Treasury gave its own report to Congress on the history of the Hopkinson claim. Aside from the lack of vouchers, the members of the board knew that "Hopkinson was not the only person consulted" on the matter of designs and therefore could not rightly claim the whole amount, and in addition, the board felt that the public was entitled to these extra services from men who drew high salaries.

Though Hopkinson's political adversaries blocked all attempts to have him paid for his services, they never denied that he made the designs. The journals of the Continental Congress clearly show that he designed the flag

The design of the first Stars and Stripes by Hopkinson had the thirteen stars arranged in a "staggered" pattern technically known as quincuncial because it is based on the repetition of a motif of five units. This arrangement inevitably results in a strongly diagonal effect. In a flag of thirteen stars, this placement produced the unmistakable outline of the crosses of St. George and of St. Andrew, as used together on the British flag. Whether this similarity was intentional or accidental, it may explain why the plainer fashion of placing the stars in three parallel rows was preferred by many Americans over the quincuncial style.

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