The header will firstly become black and then turn to white.

[TheodoreKrypton]

It will be better if the original css file can be blocked.

[ghost]

Look at #4

[babobski]

@TheodoreKrypton or you can use a different approach.
For Firefox, Chrome, Safari and Opera there is a stylish addon available, this addon you can write custom css for any web-address. If you use this approach you will not have any flashing.
Made a Gist that will revert the black bar, you can tweak it to you're likings.

The stylish addons:
FireFox
Chrome
Safari
Opera

[nhooyr]

@babobski with that css, some links aren't highlighted properly.

I'm using the following css (I took it from this repo and replaced all .great-header selectors with .header

.header.header {
    color: #333;
    background-color: #f5f5f5;
    border-bottom: 1px solid #e5e5e5
}

.header .header-search-scope {
   color: rgb(64, 120, 192);
   background-color: rgb(237, 242, 249);
   border-color: rgb(198, 215, 236);
}

.header .read-only-mode-banner {
    background-color: #f8e45f;
    border-bottom-color: #f6dc2e
}

.header .header-logo-invertocat, .header .header-logo-wordmark {
    color: #555
}

.header .notification-indicator .mail-status {
    color: #fff;
    background-image: -webkit-linear-gradient(#1cafff, #0086ce);
    background-image: linear-gradient(#1cafff, #0086ce);
    border: 2px solid #f3f3f3
}

.header .notification-indicator:hover .mail-status {
    background-color: #4078c0
}

.header .header-search-scope {
    font-size: inherit;
    color: #767676 !important;
    border-right: 1px solid #eee !important;
}

.header .scoped-search .form-control.focus .header-search-scope {
    color: #4078c0;
    background-color: #edf2f9;
    border-color: #c6d7ec
}

.header .header-nav-link {
    color: #555
}
.header .header-logo-invertocat:hover, .header .header-logo-wordmark:hover,
.header .header-nav-link:hover, .header .header-nav-link:focus {
    color: #4078c0
}

.header .header-nav-link:hover .dropdown-caret, .header .header-nav-link:focus .dropdown-caret {
    border-top-color: #4078c0
}

.header .header-search {
    font-size: 14px
}

.header .header-search-wrapper {
    background: #fff;
    box-shadow: inset 0 1px 2px rgba(0,0,0,0.075);
    border: 1px solid #ddd;
    font-size: 14px;
    min-height: 0;
}

.header .header-search-wrapper.focus {
    background: #fff;
    border-color: #51a7e8;
    outline: none;
    color: inherit;
    box-shadow: inset 0 1px 2px rgba(0, 0, 0, .075), 0 0 5px rgba(81, 167, 232, .5);
}

.header .header-search-scope {
    font-size: 12px;
    line-height: inherit;
    min-height: 0;
}

.header .header-search-input {
    min-height: 26px;
}

.header .header-search-input::-webkit-input-placeholder,
.header .header-search-input::placeholder {
    color: rgba(0,0,0,.5)
}

.header .form-control {
    color: #333 !important;
    background-color: #fff !important;
}

.header *::-webkit-input-placeholder {
    color: #767676 !important;
}
.header *:-moz-placeholder {
    /* FF 4-18 */
    color: #767676 !important;
}
.header *::-moz-placeholder {
    /* FF 19+ */
    color: #767676 !important;
}
.header *:-ms-input-placeholder {
    /* IE 10+ */
    color: #767676 !important;
}

[babobski]

@nhooyr thanks for the pointer, I will have a look this weekend. Also noticed it is not perfect jet.

[babobski]

Updated the css, so the menu links are styled correct.

[nhooyr]

I also made a style to make it easy to install.

https://userstyles.org/styles/140093/make-github-great-again

[ajayyy]

@nhooyr your script broke

[ajayyy]

Fixed plugin:

https://userstyles.org/styles/145543/make-github-great-again-2-0

[nhooyr]

Yea, I haven't been maintaining it because Github lowered the saturation of the black so it doesn't look as bad anymore for me. Glad you fixed it :)