His resignation announcement in April 2013 was viewed as a 'serious blow' for the Coalition government at a time when its controversial 'electricity market reform' (EMR) scheme was moving through the legislative process via an energy bill. Brearley was the most senior official working on the EMR scheme, which aims to promote investment in energy infrastructure.  He and close colleague Ravi Gurumurthy, reportedly 'walked out' in frustration over 'Treasury meddling'. A DECC spokesman however said that Brearley’s departure was the result of 'a long-standing agreement that he would take a career break'.
Brearley set up his own energy and climate advisory firm, Brearley Economics, in October 2013. It:
- offers advice on energy and climate change policy internationally. The main aim is to help governments and investors to manage the synergies and trade offs between cost, energy security/ access and the move to low carbon resources.
The company has supported investors to assess market and regulatory risks an opportunities in the UK and in overseas energy markets. Equally, I have supported overseas governments in their market design and in wider climate change/ energy policy design. 
He was director of the Office of Climate Change (OCC) from July 2006 until September 2009. Launched in September 2006, the OCC worked across Government to support analytical work on climate change and the development of climate change policy and strategy.
In a meeting of the Select Committee on Environmental Audit, Brearley explained the role of the Office of Climate Change:
- Mr Brearley: First of all, just to be clear the OCC is not part of Defra but actually stands between departments. We do not lead on policies.
- Q90 Mr Chayter: 'You are not formally part of Defra?'
- Mr Brearley: 'For pay and rations we are.'
- Q91 Mr Chayter: 'You are located in the same building.'
- Mr Brearley: 'We are located in the same building but are governed by six departments and funded by six departments. Our business is to support those departments to work together. We do not run policy as, for example, Defra does in parts of the Climate Change Policy, as does the DTI. I think what the OCC offers is a much more coordinated approach by Government. If you think about what we have done on the Government's arrangements, we have created a single energy environment group which is going to be supported by two cross-departmental groups to allow that to happen. I think essentially the work of the OCC should lead to a rationalisation and a simplification of what is there, rather than a duplication.' 
Prime Minister's Strategy Group
Brearley was Head of Team in the Prime Ministers Strategy Unit for four years, from 2002 – 2006.
In a Select Committee on Environmental Audit meeting held on 24 April 2007, Brearley argued against the UK including greenhouse gases from aviation or shipping in any future climate change legislation prior to there being international agreement on this issue:
- here is an issue for both shipping and aviation in the sense that these are international and, as yet, there is no agreement on how we allocate emissions between countries. One of the risks of including these within the Climate Change Bill, for example, is that we have perverse effects on policy-making itself. For example, in shipping, do we end up with ships being registered elsewhere rather than being registered in the UK? I would argue, until we have an international agreement that would allow us to understand better how we allocate emissions, it is quite a challenge for us to include those within our domestic targets." 
In the 2008 UK Climate Change Act greenhouse gas emissions from international aviation and shipping were included in the calculation of the UK total.
- University of Cambridge (Master of Philosophy (MPhil), Economics) and Glasgow University (Bachelor of Science (BSc), Mathematics and Physics_
- Jonathan Brearley, LinkedIn profile, acc 9 October 2013, NB does not appear to have been updated since his resignation in April 2013
- Terry Macalister Electricity reforms under threat as top civil servant resigns, The Guardian, Tuesday 30 April 2013, acc August 2013
- Tom Bawden, Top energy adviser walks out over 'Treasury meddling', The Independent, 3 May 2013
- Top Treasury civil servant to take up key DECC post, Business Green, 9 July 2013
- Jonathan Brearley, LinkedIn profile, accessed 12 August 2015
- , "Reconstituted Electricity Networks Strategy Group", accessed 17 March 2010
- About the OCC, OCC website, 27-11-07, accessed 17 March 2010
- "Select Committee on Environmental Audit Minutes of Evidence, "", Examination of Witnesses (Questions 86 - 99), 24 April 2007. Accessed 11/04/10
- ref needed
- "Select Committee on Environmental Audit Minutes of Evidence", House of Commons, Tuesday 24 April 2007, accessed 17 March 2010
- "Climate Change Act 2008", DECC, accessed 17 March 2010