Having obtained a medical degree with little or no knowledge of medicine, Sydenham used his position at All Souls' for the prosecution of his studies. For these, however, Oxford offered but scanty facilities. Anatomy was taught by Dr. Petty (afterwards Sir William) as deputy for the regius professor of physic, Dr. Clayton; and there is evidence that he actually obtained bodies for dissection. Medicine was taught by the regius professor, but his lectures consisted merely in reading the ancient medical classics, with which, except Hippocrates, Sydenham never showed any familiarity. There was no hospital for clinical study. From such teaching as was available he seems to have been diverted by a new commission as a captain of horse.
Sydenham has been confused in the index to the calendar of domestic state papers, 1649–51, with his brother John, Captain (afterwards Major) Sydenham, who was in 1649–50 serving in Ireland. Thomas was, however, in all probability the Captain Sydenham who in 1651 was in command of a troop of horse in Colonel Rich's regiment, forming part of three thousand horse raised out of the militia for special service. At that time John was serving under Cromwell in Scotland as a major. The only other possible Sydenham, Richard, was at this time a permanent official in London (Brit. Mus. Add. MS. 21419, fol. 226). Sydenham's troop was in the first horse regiment, of which the commissions are dated 21 April 1651. It was of some importance since urgent messages were sent by the council of state to the committee of Essex to complete his numbers (Cal. State Papers, 1651, pp. 195, 196, 514, &c.). It would appear therefore that, experienced officers being required for this large force of cavalry, Sydenham was called from his retirement and received a new commission as captain. Rich's force was ordered to lie in the neighbourhood of Leicester and Nottingham in order to secure the midland counties during Cromwell's absence in Scotland. Later in the year this force was sent for by Cromwell and placed in a post of observation on the border (Carlyle, Cromwell's Letters, Nos. 177, 180, dated 26 July and 4 Aug. 1651). When Charles II and the Scottish army marched into England, Rich's horse (with Harrison's) was ordered to follow their movements, and fought some sharp engagements in Lancashire. Either there or in the final battle of Worcester Sydenham may have seen some hard fighting, and it was possibly on one of these occasions that he was (as Andrew Broun informs us) ‘left in the field among the dead,’ and suffered the loss of blood of which he afterwards speaks. It is also to this period that we must refer a well-known anecdote of Sydenham's military life. When a captain at his lodgings in London, a drunken soldier entered his bedroom and discharged a loaded pistol at his breast. But the soldier accidentally interposed his own left hand, which was shattered by the bullet, and the captain was unhurt (Andrew Broun, from Sydenham's own lips; op. cit. p. 81).
The next piece of evidence bearing upon Sydenham's military career is a remarkable petition in his own handwriting presented to Cromwell in March 1653–4, and endorsed ‘Captain Sydenham's petition’ (State Papers, Dom. Ser. 1654, p. 14. Original in Record Office; State Papers, Interregnum, vol. lxvii. f. 37, published by Dr. Gee, St. Bartholomew's Hospital Reports, vol. xix.). The petitioner states that there was due to his brother, Major John Sydenham, slain in Scotland, a considerable arrear for his services; that the petitioner, besides being legally entitled to these arrears, had advanced money to his brother to buy horses for his services in Scotland, but all his brother's papers being lost, he could not recover these sums or arrears in the ordinary way. He himself had faithfully served the parliament with the loss of much blood, by which he was much disabled. He also insists on the services of another brother, Major Francis Sydenham, slain in the west, whose executors never received full satisfaction of his arrears. The Protector (3 March) recommended this petition in a special manner to the council, and 600l. was awarded to Sydenham, which was actually paid on 25 April 1654. The revenue committee was also directed to give him ‘such employment as he is most capable of,’ which was done five years later (Green, 1654, pp. 33, 123). In these documents he is officially styled Captain Thomas Sydenham, but evidently was not on active service after 1651.
The Protector's grant of money probably facilitated Sydenham's marriage and entrance into professional life, both of which events took place in 1655, the year in which he resigned his fellowship at All Souls. He married, at Wynford Eagle, Mary Gee, in 1655 (Parish Register of Toller Fratrum cum Wynford Eagle, examined by Rev. W. L. James; Hutchins gives 1685 in error).
Sydenham began to practise as a physician in Westminster about 1655; but it was probably in a somewhat fitful way, for he was still concerned in the politics of his party. He was candidate for Weymouth in the parliament of Richard Cromwell,
