As a Transcendentalist, he maintained a particularly close friendship with Margaret Fuller. While editing the Western Messenger in Kentucky, he commissioned her first literary review; she later became America's first woman to be a full-time literary critic. After her death, Clarke assisted Ralph Waldo Emerson in preparing Fuller's posthumous memoirs, particularly focusing on her early years. After the failure of Brook Farm, Clarke purchased the land in West Roxbury, later donating it to Abraham Lincoln for use as a training ground for soldiers.
On his 70th birthday in 1880, Clarke's friend Oliver Wendell Holmes presented a poem prepared for the occasion, titled "To James Freeman Clarke" (slightly trimmed for length here):
How few still breathe this mortal air
We called by school-boy names!
You still, whatever robe you wear,
To me are always James.
That name the kind apostle bore
Who shames the sullen creeds,
Not trusting less, but loving more,
And showing faith by deeds.
What blending thoughts our memories share!
What visions of yours and mine
Of May-days in whose morning air
The dews were golden wine,
Of vistas bright with opening day,
Whose all-awakening sun
Showed in life's landscape, far away,
The summits to be won!
His labors, — will they ever case, —
With hand and tongue and pen?
Shall wearied Nature ask release
At threescore years and ten?
Count not his years while earth has need
Of souls that Heaven inflames
With sacred seal to save, to lead, —
Long live our dear Saint James!