Bothamley began his parliamentary career in 1906 when he was appointed as a Committee Clerk, servicing the Local Bills Committee and ad hoc committees. In 1910 he was clerk for the special committee established to investigate allegations of impropriety by members of Parliament made by John Bird Hine, the member for the Stratford electorate. At that time this investigation was one of the longest parliamentary investigations in the history of the New Zealand Parliament. Bothamley was initially a sessional employee, which meant that he was not employed by Parliament during recesses, when the House of Representatives was not sitting. During such times he would find work with other government agencies such as with the Registrar-General, where he was employed as a Census Clerk in 1911/1912. It was not until 1 June 1913 that he was permanently appointed as a Committee Clerk, and on 19 July 1915 he was promoted to the position of Reader and Clerk of Bills and Papers. After World War I Bothamley returned to his position at Parliament and, on 1 June 1932, he was promoted to Second Clerk Assistant and Reader. He acted as Serjeant-at-Arms for 12 weeks following the retirement of Major H.H. Browne in 1932. On 1 July 1933 he was appointed as Clerk-Assistant, following the retirement of W.E. Dasent. For three months during 1936 Bothamley acted as Clerk of the House during the absence overseas of Thomas Donald Horn Hall. On 1 July 1945 Bothamley was appointed as Clerk of the House, following the retirement of Thomas Donald Horn Hall. Hall was the first legally qualified Clerk; at the time of his appointment in 1930, Speaker of the House, Sir Charles Ernest Statham, had insisted that the holder of the role should be a qualified lawyer, and this view was endorsed by the subsequent Speaker William Edward Barnard. As Bothamley did not have a legal qualification and was 65 years of age at the time of his appointment as Clerk of the House, he was appointed on the understanding that he would retire "within a reasonable time after the termination of hostilities". While Bothamley was Clerk of the House the end of the 27th New Zealand Parliament's three-year term was inadvertently reached, causing the Parliament to run its full legal course for the first time. The effect of this was that the 27th Parliament was allowed to expire before it could be dissolved by the Governor-General, thereby casting doubt on the validity of legislation that was given the Royal Assent after Parliament had expired, and on the legality of subsequent parliamentary elections. These matters were eventually considered by the Court of Appeal in the case Simpson v Attorney-General, with the court upholding the validity of both matters, despite finding that, due to Parliament being allowed to expire, the subsequent elections had not been held in accordance with the timetable required by the Electoral Act 1927. After serving as Clerk of the House for one year and four months, Bothamley retired on 31 October 1946, at 66 years of age, following 40 years' service.
Bothamley dynasty
The Bothamley family had a close association with the New Zealand Parliament that spanned almost 80 years. In 1871 Grafton's father Arthur Thomas Bothamley joined the office of the New Zealand Legislative Council serving as both Clerk-Assistant and then Clerk of the Legislative Council. He was also Private Secretary to Premier Sir John Hall, Clerk of Parliaments, and for 45 years he was the Legislative Council's Gentleman Usher of the Black Rod. Grafton's brother Charles Mildmay Bothamley began working in Parliament in 1917 and retired as the last Clerk of the New Zealand Legislative Council and Clerk of Parliaments in 1950.