Kent-based McNaughton reached 38th position and is the only merchant to appear in the list, where it also collected an award for Outstanding Environmental Performance.
The Sunday Times said the company has developed an "extensive range" of environmentally responsible products, and used as many innovations as possible to reduce its own impact.
Howard Browning, McNaughton director for corporate responsibility, said: "This award has been subject to independent scrutiny by Bureaux Veritas, and importantly, 30% of the award marks were based solely on the confidential views of colleagues.
"For this there had to be a minimum of 40% participation, which makes it all the more meaningful."
According to the staff survey, 78% of bosses are committed to the environment, 82% know what ISO 14001 is and 85% "think green".
The company has also worked with the Edinburgh Centre for Carbon Management to develop a carbon calculator for paper production and delivery.
Elsewhere, London-based Allsignsgroup scooped the sixth greenest manufacturer in the UK award and was placed 45th in the list.
As part of its aim to achieve ISO 14001, the company has introduced a recover, recycle and re-use scheme and now recycles 65% of its annual waste.
Managing director Mike Freely said: "Our industry can be very wasteful and we were once part of that, putting some 200 tonnes of plastic into landfill per year.
"However, we have turned that on its head and now 65% of our wastage is recycled."
Staff gave the business green scores of 99% and 96% respectively for knowing where to put waste and what waste goes where.
The Sunday Times Green List was published on 24 May and the rankings were derived from the employer survey and the employee survey.
Paper group and printer in Sunday Times 'green' list
Environmental credentials at paper merchant James McNaughton Group and large-format printer Allsignsgroup have been recognised in the latest Sunday Times 60 Best Green Companies 2009.