Phineas wished to follow the progress of the Triumph, but finding his brother Joseph unwilling to retain him in his employment, he followed Baker to Deptford, and continued to work at the Repulse until she was finished, launched, and set sail on her voyage, at the end of April, 1596. This was the leading ship of the squadron which set sail for Cadiz, under the command of the Earl of Essex and the Lord Admiral Howard, and which did so much damage to the forts and shipping of Philip II. of Spain.

During the winter months, while the work was in progress, Pett spent the leisure of his evenings in perfecting himself in learning, especially in drawing, cyphering, and mathematics, for the purpose, as he says, of attaining the knowledge of his profession. His master, Mr. Baker, gave him every encouragement, and from his assistance, he adds, "I must acknowledge I received my greatest lights." The Lord Admiral was often present at Baker's house. Pett was importuned to set sail with the ship when finished, but he preferred remaining at home. The principal reason, no doubt, that restrained him at this moment from seeking the patronage of the great, was the care of his two sisters,[19] who, having fled from the house of their barbarous stepfather, could find no refuge but in that of their brother Phineas. Joseph refused to receive them, and Peter of Wapping was perhaps less able than willing to do so.

In April, 1597, Pett had the advantage of being introduced to Howard, Earl of Nottingham, then Lord High Admiral of England. This, he says, was the first beginning of his rising. Two years later, Howard recommended him for employment in purveying plank and timber in Norfolk and Suffolk for shipbuilding purposes. Pett accomplished his business satisfactorily, though he had some malicious enemies to contend against. In his leisure, he began to prepare models of ships, which he rigged and finished complete. He also proceeded with the study of mathematics. The beginning of the year 1600 found Pett once more out of employment; and during his enforced idleness, which continued for six months, he seriously contemplated abandoning his profession and attempting to gain "an honest and convenient maintenance" by joining a friend in purchasing a caravel (a small vessel), and navigating it himself.

He was, however, prevented from undertaking this enterprise by a message which he received from the Court, then stationed at Greenwich. The Lord High Admiral desired to see him; and after many civil compliments, he offered him the post of keeper of the plankyard at Chatham. Pett was only too glad to accept this offer, though the salary was small. He shipped his furniture on board a hoy of Rainham, and accompanied it down the Thames to the junction with the Medway. There he escaped a great danger—one of the sea perils of the time. The mouths of navigable rivers were still infested with pirates; and as the hoy containing Pett approached the Nore about three o'clock in the morning, and while still dark, she came upon a Dunkirk picaroon, full of men. Fortunately the pirate was at anchor; she weighed and gave chase, and had not the hoy set full sail, and been impelled up the Swale by a fresh wind, Pett would have been taken prisoner, with all his furniture.[20]

Arrived at Chatham, Pett met his brother Joseph, became reconciled to him, and ever after they lived together as loving brethren. At his brother's suggestion, Pett took a lease of the Manor House, and settled there with his sisters. He was now in the direct way to preferment. Early in the following year (March, 1601) he succeeded to the place of assistant to the principal master shipwright at Chatham, and undertook the repairs of Her Majesty's ship The Lion's Whelp, and in the next year he new-built the Moon enlarging her both in length and breadth.

At the accession of James I. in 1603, Pett was commanded by the Lord High Admiral with all possible speed to build a little vessel for the young Prince Henry, eldest son of His Majesty. It was to be a sort of copy of the Ark Royal, which was the flagship of the Lord High Admiral when he defeated the Spanish Armada. Pett proceeded to accomplish the order with all dispatch. The little ship was in length by the keel 28 feet, in breadth 12 feet, and very curiously garnished within and without with painting and carving. After working by torch and candle light, night and day, the ship was launched, and set sail for the Thames, with the noise of drums, trumpets, and cannon, at the beginning of March, 1604. After passing through a great storm at the Nore, the vessel reached the Tower, where the King and the young Prince inspected her with delight. She was christened Disdain by the Lord High Admiral, and Pett was appointed captain of the ship.

After his return to Chatham, Pett, at his own charge, built a small ship at Gillingham, of 300 tons, which he launched in the same year, and named the Resistance. The ship was scarcely out of hand, when Pett was ordered to Woolwich, to prepare the Bear and other vessels for conveying his patron, the Lord High Admiral, as an Ambassador Extraordinary to Spain, for the purpose of concluding peace, after a strife of more than forty years. The Resistance was hired by the Government as a transport, and Pett was put in command. He seems to have been married at this time, as he mentions in his memoir that he parted with his wife and children at Chatham on the 24th of March, 1605, and that he sailed from Queenborough on Easter Sunday.

During the voyage to Lisbon the Resistance became separated from the Ambassador's squadron, and took refuge in Corunna. She then set sail for Lisbon, which she reached on the 24th of April; and afterwards for St. Lucar, on the Guadalquiver, near Seville, which she reached on the 11th of May following. After revisiting Corunna, "according to instructions," on the homeward voyage, Pett directed his course for England, and reached Rye on the 26th of June, "amidst much rain, thunder, and lightning." In the course of the same year, his brother Joseph died, and Phineas succeeded to his post as master shipbuilder at Chatham. He was permitted, in conjunction with one Henry Farvey and three others, to receive the usual reward of 5s. per ton for building five new merchant ships,[21] most probably for East Indian commerce, now assuming large dimensions. He was despatched by the Government to Bearwood, in Hampshire, to make a selection of timber from the estate of the Earl of Worcester for the use of the navy, and on presenting his report 3000 tons were purchased. What with his building of ships, his attendance on the Lord Admiral to Spain, and his selection of timber for the Government, his hands seem to have been kept very full during the whole of 1605.

In July, 1606, Pett received private instructions from the Lord High Admiral to have all the King's ships "put into comely readiness" for the reception of the King of Denmark, who was expected on a Royal visit. "Wherein," he says, "I strove extraordinarily to express my service for the honour of the kingdom; but by reason the time limited was short, and the business great, we laboured night and day to effect it, which accordingly was done, to the great honour of our sovereign king and master, and no less admiration of all strangers that were eye-witnesses to the same." The reception took place on the 10th of August, 1606.

Shortly after the departure of His Majesty of Denmark, four of the Royal ships—the Ark, Victory, Golden Lion, and Swiftsure—were ordered to be dry-docked; the two last mentioned at Deptford, under charge of Matthew Baker; and the two former at Woolwich, under that of Pett. For greater convenience, Pett removed his family to Woolwich. After being elected and sworn Master of the Company of Shipwrights, he refers in his manuscript, for the first time, to his magnificent and original design of the Prince Royal.[22]