Waidyaratne joined the Ceylon Army on 26 June 1959, as a cadet officer and received his officer training at Royal Military Academy, Sandhurst. On 28 July 1961, he was commissioned as a second lieutenant in the 1st Reconnaissance Regiment, Ceylon Armoured Corps. He served with the 1st Reconnaissance Regiment during the 1971 JVP insurrection and in 1973, he attended the Defence Services Staff College in Wellington.