The cross-industry National Apprenticeship Awards ceremony was held at London's Grosvenor House, with Cain fighting off competition from hundreds of candidates around England for the prize.
The awards, now in their 12th year, are run by the National Apprenticeship Service and recognise excellence in two areas: businesses that grow their own talent with apprentices and apprentices who have made a significant contribution to their workplaces.
Cain was put forward for the national title after being named apprenticeship champion for the Central Eastern region in November last year. He was chosen in recognition of the outstanding contribution he has made to apprenticeships since starting out as a Sunderland parks apprentice in 1980.
He went on to support new apprentices working in The Royal Parks in the 1990s, developing their site-based training programme before becoming the driving force behind apprenticeships at John O'Conner.
On accepting the award, Cain said: "My apprenticeship with Sunderland Parks Department has been the foundation for over 30 successful years in the horticulture industry, providing personal and professional fulfilment. My progression from apprentice to operations director at John O'Conner is a testament to the potential of apprenticeships and my biggest achievement. It's evidence a university route is not the only option to exceptional careers, hence why I champion apprenticeships in addition to my job role within John O'Conner and externally."
He added that he is "delighted" to dedicate personal time to promote the cause, and has passionately encouraged John O'Conner to embrace an apprenticeship culture.
"I believe my story of progressing from an apprentice to operations director enables me to offer strong experience [and] advice to apprentices. I always have an open door for anyone, not just new young apprentices but existing staff. Apprenticeships are for everyone."
Skills minister Nick Boles and employment minister Priti Patel both congratulated Cain on his win.
Boles said: "Apprenticeships truly are set to be one of the great success stories of the decade, and Neil is a worthy ambassador. We are committed to three million apprenticeships by 2020 so that even more businesses and young people alike can follow Neil's lead and reap the benefits of apprenticeships."
The awards were presented by Nadhim Zahawi, the Prime Minister's apprenticeship adviser.
Zahawi highlighted the Government's commitment to apprenticeship training, saying: "Good quality apprenticeships create a fairer society by giving hard working young people the chance to aim for their dream job whilst playing their part in building a stronger economy for Britain.
"There are many examples of excellent apprenticeships and apprentices in England and these winners are the best of the best. I congratulate Neil on his success. It's an honour to have been part of these awards; to play a small part in recognising the effort of so many great businesses and to reward apprentices for their hard work and dedication."
