Use the -t and -T switches to force the interactive and the non-interactive mode, respectively. Note that providing a command using the -m switch or directly on command-line implies a non-interactive mode, while using the standard input uses an interactive mode by default. (of course, you will use redirection mechanism of your language, instead of the <). Or using its standard input plink.exe < c:\local\path\command.txt Free & Safe Download for Windows PC/laptop 3.02 MB. It works with Windows XP64 / Vista64 / Windows 7 64 / Windows 8 64 / Windows 10 64. And in addition to those, you can specify your command directly on its command like: plink.exe /home/user/myscript.sh Download & install the latest offline installer version of PuTTY for Windows PC / laptop. The Plink ( plink.exe) has the same command-line arguments as PuTTY. The Plink is a part of PuTTY package, so everyone who has PuTTY should have Plink too. Though for automation, your better use the Plink command-line connection tool, instead of the GUI PuTTY application, as you have already found out. Where the commands.txt will, in your case, contain a path to your shell script, like: /home/user/myscript.sh PuTTY has the -m switch, that you can use to provide a path to a file with a list of commands to execute: putty.exe -m c:\local\path\commands.txt