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I got sucked in my project where I have upload some files at location ~siteurl/_catalogs/theme by using client site scripting like JS/JQuery/REST/CSOM ? I searched a lot but no luck. Please help me. It's on-premise 2016 server. We are building this solution as third party user is managing our servers and we cannot place these file directly by server access. Also,uploading a files from browser is a option but want to do this by script as there are 1000+ site collection. And manual process is not possible. At least should I am able to upload the files using client script.

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The easiest way is to use CSOM. If it will run on the server, then just add reference to Microsoft.SharePoint.Client and Microsoft.SharePoint.Clinet.Runtime. If it will run on some client computer, then install SharePoint Server 2013 Client Components SDK and add the same references.

using Microsoft.SharePoint.Client;

namespace StackExchange.ConsoleApp
{
    class Program
    {
        static void Main(string[] args)
        {
            using (ClientContext cc = new ClientContext("https://sharepoint.domain.com"))
            {
                // Load only ServerRelativeUrl
                cc.Load(cc.Web, x => x.ServerRelativeUrl);
                cc.ExecuteQuery();

                // Get list by url
                List list = cc.Web.GetList(cc.Web.ServerRelativeUrl.TrimEnd('/') + "/_catalogs/theme");

                // Create file the library
                File file = list.RootFolder.Files.Add(new FileCreationInformation()
                {
                    // You can also add content through Stream using ContentStream
                    Content = new byte[] { 0, 1, 2, 3 },
                    Url = "file-name.txt"
                });

                cc.ExecuteQuery();
            }
        }
    }
}

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